adjust galaxy wrappers to use scriptmanager_macros

Adjust wrappers to use the tool macros for the scriptmanager jar filename and requirements/dependencies
CEGRcode · Aug 2, 2024 · b6171a0 · b6171a0
1 parent a751b2d
commit b6171a0
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Showing 15 changed files with 84 additions and 38 deletions.
diff --git a/galaxy/wrapper/scriptmanager_aggregate-data.xml b/galaxy/wrapper/scriptmanager_aggregate-data.xml
@@ -1,11 +1,14 @@
 <tool id="scriptmanager_aggregate-data" name="ScriptManager: Aggregate Data"
     version="0.1.0+galaxy0" python_template_version="3.5" profile="21.05">
     <description> Aggregate Data </description>
+    <macros>
+        <import>scriptmanager_macros.xml</import>
+    </macros>
     <requirements>
-        <requirement type="package" version="11.0.11">openjdk</requirement>
+        <expand macro="requirement_openjdk" />
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
-        java -jar $__tool_directory__/ScriptManager-v0.14.jar read-analysis aggregate-data
+        java -jar $__tool_directory__/@JAR_FILENAME@ read-analysis aggregate-data
         
         #if str($output_file_name.bool) == "Yes" :
             -o "$output_file_name.directory"

diff --git a/galaxy/wrapper/scriptmanager_composite-plot.xml b/galaxy/wrapper/scriptmanager_composite-plot.xml
@@ -1,11 +1,14 @@
 <tool id="scriptmanager_composite-plot" name="ScriptManager: Composite Plot"
     version="0.1.0+galaxy0" python_template_version="3.5" profile="21.05">
     <description> Composite Plot </description>
-   <requirements>
-        <requirement type="package" version="11.0.11">openjdk</requirement>
+    <macros>
+        <import>scriptmanager_macros.xml</import>
+    </macros>
+    <requirements>
+        <expand macro="requirement_openjdk" />
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
-        java -jar $__tool_directory__/ScriptManager-v0.14.jar figure-generation composite-plot
+        java -jar $__tool_directory__/@JAR_FILENAME@ figure-generation composite-plot
                 
         #if str($output_file_name.bool) == "Yes" :
             -o "$output_file_name.directory"

diff --git a/galaxy/wrapper/scriptmanager_convert-bed-chr-names.xml b/galaxy/wrapper/scriptmanager_convert-bed-chr-names.xml
@@ -1,13 +1,16 @@
 <tool id="scriptmanager_convert-bed-chr-names" name="ScriptManager: Convert BED Chr Names"
     version="0.1.0+galaxy0" python_template_version="3.5" profile="21.05">
     <description> Convert BED Chr Names </description>
-   <requirements>
-        <requirement type="package" version="11.0.11">openjdk</requirement>
+    <macros>
+        <import>scriptmanager_macros.xml</import>
+    </macros>
+    <requirements>
+        <expand macro="requirement_openjdk" />
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
         ln -s "$input" "temp_input.bed" &&
         
-        java -jar $__tool_directory__/ScriptManager-v0.14.jar file-utilities convert-bed-genome
+        java -jar $__tool_directory__/@JAR_FILENAME@ file-utilities convert-bed-genome
                 
         #if str($output_file_name.bool) == "Yes" :
             -o "$output_file_name.file_name"

diff --git a/galaxy/wrapper/scriptmanager_convert-gff-chr-names.xml b/galaxy/wrapper/scriptmanager_convert-gff-chr-names.xml
@@ -1,13 +1,16 @@
 <tool id="scriptmanager_convert-gff-chr-names" name="ScriptManager: Convert GFF Chr Names"
     version="0.1.0+galaxy0" python_template_version="3.5" profile="21.05">
     <description> Convert GFF Chr Names </description>
-   <requirements>
-        <requirement type="package" version="11.0.11">openjdk</requirement>
+    <macros>
+        <import>scriptmanager_macros.xml</import>
+    </macros>
+    <requirements>
+        <expand macro="requirement_openjdk" />
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
         ln -s "$input" "temp_input.gff" &&
 
-        java -jar $__tool_directory__/ScriptManager-v0.14.jar file-utilities convert-gff-genome
+        java -jar $__tool_directory__/@JAR_FILENAME@ file-utilities convert-gff-genome
                 
         #if str($output_file_name.bool) == "Yes" :
             -o "$output_file_name.file_name"

diff --git a/galaxy/wrapper/scriptmanager_cross-corr.xml b/galaxy/wrapper/scriptmanager_cross-corr.xml
@@ -1,15 +1,17 @@
 <tool id="scriptmanager_cross-corr" name="ScriptManager: Cross Correlation"
     version="0.1.0+galaxy0" python_template_version="3.5" profile="21.05">
     <description> BAM Cross Correlation </description>
+    <macros>
+        <import>scriptmanager_macros.xml</import>
+    </macros>
     <requirements>
-        <requirement type="package" version="11.0.11">openjdk</requirement>
+        <expand macro="requirement_openjdk" />
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
         ln -s "$input" "temp_input.bam" &&
         samtools index "temp_input.bam" &&
 
-        
-        java -jar $__tool_directory__/ScriptManager-v0.14-bugfix153.jar bam-statistics cross-corr
+        java -jar $__tool_directory__/@JAR_FILENAME@ bam-statistics cross-corr
         
         #if str($output_file_name.bool) == "Yes" :
             -o "$output_file_name.file_name"

diff --git a/galaxy/wrapper/scriptmanager_filter-bed.xml b/galaxy/wrapper/scriptmanager_filter-bed.xml
@@ -1,13 +1,16 @@
 <tool id="scriptmanager_filter-bed" name="ScriptManager: Filter Bed"
     version="0.1.0+galaxy0" python_template_version="3.5" profile="21.05">
     <description> Filter BED by Proximity </description>
+    <macros>
+        <import>scriptmanager_macros.xml</import>
+    </macros>
     <requirements>
-        <requirement type="package" version="11.0.11">openjdk</requirement>
+        <expand macro="requirement_openjdk" />
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
         ln -s "$input" "temp_input.bed" &&
         
-        java -jar $__tool_directory__/ScriptManager-v0.14.jar peak-analysis filter-bed
+        java -jar $__tool_directory__/@JAR_FILENAME@ peak-analysis filter-bed
         
         #if str($output_file_name.bool) == "Yes" :
             -o "$output_file_name.file_name"

diff --git a/galaxy/wrapper/scriptmanager_filter-pip-seq.xml b/galaxy/wrapper/scriptmanager_filter-pip-seq.xml
@@ -1,9 +1,12 @@
 <tool id="scriptmanager_filter-pip-seq" name="ScriptManager: Filter Pip Seq"
     version="0.1.0+galaxy0" python_template_version="3.5" profile="21.05">
     <description> Filter Pip Seq </description>
+    <macros>
+        <import>scriptmanager_macros.xml</import>
+    </macros>
     <requirements>
-        <requirement type="package" version="1.10">samtools</requirement>
-        <requirement type="package" version="11.0.11">openjdk</requirement>
+        <expand macro="requirement_openjdk" />
+        <expand macro="requirement_samtools" />
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
         ln -s "$input1" "temp_input1.fasta" &&
@@ -12,7 +15,7 @@
         samtools faidx "temp_input1.fasta" &&
         samtools index "temp_input2.bam" &&
         
-        java -jar $__tool_directory__/ScriptManager-v0.14.jar bam-manipulation filter-pip-seq
+        java -jar $__tool_directory__/@JAR_FILENAME@ bam-manipulation filter-pip-seq
 
         #if str($output_file_name.bool) == "Yes" :
             -o "$output_file_name.file_name"

diff --git a/galaxy/wrapper/scriptmanager_peak-align-ref.xml b/galaxy/wrapper/scriptmanager_peak-align-ref.xml
@@ -1,14 +1,17 @@
 <tool id="scriptmanager_peak_align_ref" name="ScriptManager: Align BED to Reference"
     version="0.1.0+galaxy0" python_template_version="3.5" profile="21.05">
     <description> Align BED to Reference </description>
+    <macros>
+        <import>scriptmanager_macros.xml</import>
+    </macros>
     <requirements>
-        <requirement type="package" version="11.0.11">openjdk</requirement>
+        <expand macro="requirement_openjdk" />
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
         ln -s "$input_peak" "temp_input_peak.bed" &&
         ln -s "$input_ref" "temp_input_ref.bed" &&
 
-        java -jar $__tool_directory__/ScriptManager-v0.14.jar peak-analysis peak-align-ref
+        java -jar $__tool_directory__/@JAR_FILENAME@ peak-analysis peak-align-ref
         
         #if str($output_file_name.bool) == "Yes" :
             -o "$output_file_name.file_name"

diff --git a/galaxy/wrapper/scriptmanager_rand-coord.xml b/galaxy/wrapper/scriptmanager_rand-coord.xml
@@ -1,11 +1,14 @@
 <tool id="scriptmanager_rand-coord" name="ScriptManager: Random Coordinate Generator"
     version="0.1.0+galaxy0" python_template_version="3.5" profile="21.05">
     <description> Random Coordinate Generator </description>
+    <macros>
+        <import>scriptmanager_macros.xml</import>
+    </macros>
     <requirements>
-        <requirement type="package" version="11.0.11">openjdk</requirement>
+        <expand macro="requirement_openjdk" />
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
-        java -jar $__tool_directory__/ScriptManager-v0.14.jar peak-analysis rand-coord
+        java -jar $__tool_directory__/@JAR_FILENAME@ peak-analysis rand-coord
 
         "$genome_name"
         

diff --git a/galaxy/wrapper/scriptmanager_randomize-fasta.xml b/galaxy/wrapper/scriptmanager_randomize-fasta.xml
@@ -1,13 +1,16 @@
 <tool id="scriptmanager_randomize-fasta" name="ScriptManager: Randomize Fasta"
     version="0.1.0+galaxy0" python_template_version="3.5" profile="21.05">
     <description> Randomize Fasta </description>
+    <macros>
+        <import>scriptmanager_macros.xml</import>
+    </macros>
     <requirements>
-        <requirement type="package" version="11.0.11">openjdk</requirement>
+        <expand macro="requirement_openjdk" />
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
         ln -s "$input" "temp_input.fasta" &&
 
-        java -jar $__tool_directory__/ScriptManager-v0.14.jar sequence-analysis randomize-fasta
+        java -jar $__tool_directory__/@JAR_FILENAME@ sequence-analysis randomize-fasta
         
         #if str($output_file_name.bool) == "Yes" :
             -o "$output_file_name.file_name"

diff --git a/galaxy/wrapper/scriptmanager_scale-matrix.xml b/galaxy/wrapper/scriptmanager_scale-matrix.xml
@@ -1,11 +1,14 @@
 <tool id="scriptmanager_scale-matrix" name="ScriptManager: Scale Matrix"
     version="0.1.0+galaxy0" python_template_version="3.5" profile="21.05">
     <description> Scale Matrix Data </description>
+    <macros>
+        <import>scriptmanager_macros.xml</import>
+    </macros>
     <requirements>
-        <requirement type="package" version="11.0.11">openjdk</requirement>
+        <expand macro="requirement_openjdk" />
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
-        java -jar $__tool_directory__/ScriptManager-v0.14.jar read-analysis scale-matrix
+        java -jar $__tool_directory__/@JAR_FILENAME@ read-analysis scale-matrix
 
         #if str($output_file_name.bool) == "Yes" :
             -o "$output_file_name.file_name"

diff --git a/galaxy/wrapper/scriptmanager_scaling-factor.xml b/galaxy/wrapper/scriptmanager_scaling-factor.xml
@@ -1,18 +1,22 @@
 <tool id="scriptmanager_scaling-factor" name="ScriptManager: Scaling Factor"
     version="0.1.0+galaxy0" python_template_version="3.5" profile="21.05">
     <description> Calculate Scaling Factor </description>
+    <macros>
+        <import>scriptmanager_macros.xml</import>
+    </macros>
     <requirements>
-        <requirement type="package" version="1.10">samtools</requirement>
-        <requirement type="package" version="11.0.11">openjdk</requirement>
+        <expand macro="requirement_openjdk" />
+        <expand macro="requirement_samtools" />
     </requirements>
+
     <command detect_errors="exit_code"><![CDATA[
         ln -s "$input1" "temp_input.bam" &&
         ln -s "$input2" "temp_control.bam" &&
 
         samtools index "temp_input.bam" &&
         samtools index "temp_control.bam" &&
         
-        java -jar $__tool_directory__/ScriptManager-v0.14.jar read-analysis scaling-factor
+        java -jar $__tool_directory__/@JAR_FILENAME@ read-analysis scaling-factor
 
         #if str($output_file_name.bool) == "Yes" :
             -o "$output_file_name.file_name"

diff --git a/galaxy/wrapper/scriptmanager_search-motif.xml b/galaxy/wrapper/scriptmanager_search-motif.xml
@@ -1,13 +1,16 @@
 <tool id="scriptmanager_search-motif" name="ScriptManager: Search Motif in FASTA file with Mismatch"
     version="0.1.0+galaxy0" python_template_version="3.5" profile="21.05">
     <description> Search Motif in FASTA file with Mismatch </description>
+    <macros>
+        <import>scriptmanager_macros.xml</import>
+    </macros>
     <requirements>
-        <requirement type="package" version="11.0.11">openjdk</requirement>
+        <expand macro="requirement_openjdk" />
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
         ln -s "$input" "temp_input.fasta" &&
         
-        java -jar $__tool_directory__/ScriptManager-v0.14.jar sequence-analysis search-motif
+        java -jar $__tool_directory__/@JAR_FILENAME@ sequence-analysis search-motif
         
         #if str($output_file_name.bool) == "Yes" :
             -o "$output_file_name.file_name"

diff --git a/galaxy/wrapper/scriptmanager_signal-dup.xml b/galaxy/wrapper/scriptmanager_signal-dup.xml
@@ -1,14 +1,18 @@
-<tool id="scriptmanager_signal-dup" name="ScriptManager: Signal Duplication"
+<tool id="scriptmanager_signal-dup" name="(DONOTUSE) ScriptManager: Signal Duplication"
     version="0.1.0+galaxy0" python_template_version="3.5" profile="21.05">
     <description> Signal Duplication </description>
+    <macros>
+        <import>scriptmanager_macros.xml</import>
+    </macros>
     <requirements>
-        <requirement type="package" version="11.0.11">openjdk</requirement>
+        <expand macro="requirement_openjdk" />
     </requirements>
+
     <command detect_errors="exit_code"><![CDATA[
         ln -s "$input_gff" "temp_input1.gff" &&
         ln -s "$input_bam" "temp_input2.bam" &&
 
-        java -jar $__tool_directory__/ScriptManager-v0.14.jar peak-analysis signal-dup
+        java -jar $__tool_directory__/@JAR_FILENAME@ peak-analysis signal-dup
 
         #if str($output_file_name.bool) == "Yes" :
             -o "$output_file_name.file_name"

diff --git a/galaxy/wrapper/scriptmanager_tile-genome.xml b/galaxy/wrapper/scriptmanager_tile-genome.xml
@@ -1,11 +1,14 @@
 <tool id="scriptmanager_tile-genome" name="ScriptManager: Genomic Coordinate Tiling Generator"
     version="0.1.0+galaxy0" python_template_version="3.5" profile="21.05">
     <description> Genomic Coordinate Tiling Generator </description>
+    <macros>
+        <import>scriptmanager_macros.xml</import>
+    </macros>
     <requirements>
-        <requirement type="package" version="11.0.11">openjdk</requirement>
+        <expand macro="requirement_openjdk" />
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
-        java -jar $__tool_directory__/ScriptManager-v0.14.jar peak-analysis tile-genome
+        java -jar $__tool_directory__/@JAR_FILENAME@ peak-analysis tile-genome
 
         "$genome_name"
         
@@ -20,7 +23,7 @@
         #if str($window) != "200" :
             -w "$window"
         #end if
-        
+
     ]]></command>
     <inputs>
         <param type="select" name="genome_name" label="Genome Name">