Merge pull request #171 from CEGRcode/galaxy-wrappers-corepipeline

Complete draft set of galaxy wrappers including ones used for the core pipeline
CEGRcode · Aug 2, 2024 · 2e2f688 · 2e2f688
2 parents 31734cb + b6171a0
commit 2e2f688
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Showing 40 changed files with 924 additions and 882 deletions.
diff --git a/.DS_Store b/.DS_Store
diff --git a/galaxy/.DS_Store b/galaxy/.DS_Store
diff --git a/galaxy/wrapper/.DS_Store b/galaxy/wrapper/.DS_Store
diff --git a/galaxy/wrapper/README.md b/galaxy/wrapper/README.md
@@ -45,14 +45,27 @@ sudo git clone https://github.com/CEGRcode/scriptmanager-galaxy_tools.git
 2. Tell galaxy where to look for scriptmanager tools by adding the following section to `/mnt/mountpoint/srv/galaxy/config/local_tool_conf.xml` file.
 
 ```
-<section id="ScriptManager" name="ScriptManager" > 
-
-       <tool file="scriptmanager-galaxy_tools/script_manager_heatmap.xml" />
-       <tool file="scriptmanager-galaxy_tools/script_manager_tag_pileup.xml" />
-       <tool file="scriptmanager-galaxy_tools/scriptmanager_heatmap_add_label.xml" /> 
-       <tool file="scriptmanager-galaxy_tools/script_manager_4color.xml" />
-       
-</section>
+    <section id="scriptmanager-owlang" name="ScriptManager" > 
+        <tool file="scriptmanager-owlang/scriptmanager_bam-correlation.xml" />
+        <tool file="scriptmanager-owlang/scriptmanager_bam-to-bed.xml" />
+        <tool file="scriptmanager-owlang/scriptmanager_bam-to-bedgraph.xml" />
+        <tool file="scriptmanager-owlang/scriptmanager_bam-to-gff.xml" />
+        <tool file="scriptmanager-owlang/scriptmanager_bam-to-scidx.xml" />
+        <tool file="scriptmanager-owlang/scriptmanager_bed-to-gff.xml" />
+        <tool file="scriptmanager-owlang/scriptmanager_expand-bed.xml" />
+        <tool file="scriptmanager-owlang/scriptmanager_expand-gff.xml" />
+        <tool file="scriptmanager-owlang/scriptmanager_four-color.xml" />
+        <tool file="scriptmanager-owlang/scriptmanager_gff-to-bed.xml" />
+        <tool file="scriptmanager-owlang/scriptmanager_heatmap.xml" />
+        <tool file="scriptmanager-owlang/scriptmanager_label-heatmap.xml" />
+        <tool file="scriptmanager-owlang/scriptmanager_merge-heatmap.xml" />
+        <tool file="scriptmanager-owlang/scriptmanager_pe-stat.xml" />
+        <tool file="scriptmanager-owlang/scriptmanager_se-stat.xml" />
+        <tool file="scriptmanager-owlang/scriptmanager_shift-coord.xml" />
+        <tool file="scriptmanager-owlang/scriptmanager_sort-bed.xml" />
+        <tool file="scriptmanager-owlang/scriptmanager_sort-gff.xml" />
+        <tool file="scriptmanager-owlang/scriptmanager_tag-pileup.xml" />
+    </section>
 ```
 
 3. Restart Galaxy
@@ -66,3 +79,4 @@ sudo git clone https://github.com/CEGRcode/scriptmanager-galaxy_tools.git
 
 
 Thank you to Ali Nematbakhsh(https://github.com/AliNemat) and Audrey Sackey(https://github.com/Adjekai) for their initial work in writing these wrappers.
+
diff --git a/galaxy/wrapper/macros.xml b/galaxy/wrapper/macros.xml
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_bam-correlation.xml b/galaxy/wrapper/scriptmanager_bam-correlation.xml
@@ -1,12 +1,12 @@
-<tool id="bamcorrelation_test" name="ScriptManager: BAM Correlation" version="0.1.0+galaxy0" python_template_version="3.5" profile="21.05">
+<tool id="scriptmanager_bam-correlation" name="ScriptManager: BAM Correlation" version="0.1.0" profile="22.01" >
     <description> Genome-Genome correlations for replicate comparisons given multiple sorted and indexed (BAI) BAM files. </description>
-    <requirements>
-        <requirement type="package" version="11.0.11">openjdk</requirement>
-        <requirement type="package" version="1.9">samtools</requirement>
-    </requirements>
     <macros>
-        <import>macros.xml</import>
+        <import>scriptmanager_macros.xml</import>
     </macros>
+    <requirements>
+        <expand macro="requirement_openjdk" />
+        <expand macro="requirement_samtools" />
+    </requirements>
     <command detect_errors="exit_code"><![CDATA[
         ln -s '$BAM' bamfile.bam &&
         ln -s '$output1' output1.tab &&
@@ -18,9 +18,10 @@
             #end if
         #end if
 
-        java -jar $__tool_directory__/ScriptManager-v0.14-dev.jar bam-statistics bam-correlation 
+        java -jar $__tool_directory__/@JAR_FILENAME@ bam-statistics bam-correlation
+
+
 
-        
         #if str($read) == "read_1" :
             -1
         #else if str($read) == "read_2" :
@@ -33,14 +34,14 @@
 
         -b "$bin_size"
         --cpu "$cpu"
-        
-        '$output1' 
-        
+
+        '$output1'
+
         -t "$tag_shift"
-        
+
         bamfile.bam
 
-        
+
     ]]></command>
     <inputs>
         <param type="data" name="BAM" format="bam" multiple="True" label="Input BAM files"/>
@@ -61,7 +62,8 @@
     </outputs>
     <help>
 **What it does**
-Genome-Genome correlations for replicate comparisons given multiple sorted and indexed (BAI) BAM files.
 
+Genome-Genome correlations for replicate comparisons given multiple sorted and indexed (BAI) BAM files.
     </help>
-</tool>
+    <expand macro="citations_pearc" />
+</tool>
diff --git a/galaxy/wrapper/scriptmanager_bam-to-bed.xml b/galaxy/wrapper/scriptmanager_bam-to-bed.xml
@@ -1,21 +1,27 @@
-<tool id="scriptmanager_bam-to-bed" name="ScriptManager: Convert BAM to BED" version="0.1.0+galaxy0" python_template_version="3.5" profile="21.05">
+<tool id="scriptmanager_bam-to-bed" name="ScriptManager: Convert BAM to BED" version="0.1.0" profile="22.01" >
     <description> Convert BAM file to BED file </description>
+    <macros>
+        <import>scriptmanager_macros.xml</import>
+    </macros>
    <requirements>
-        <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 '$BAM' bamfile.bam &&
-        ln -s '$output1' output1.bed &&
-        #if $BAM.is_of_type('bam'):
-            #if str( $BAM.metadata.bam_index ) != "None":
-                    ln -s '${BAM.metadata.bam_index}' bamfile.bam.bai &&
+        ln -s '$input' bamfile.bam &&
+        #if $input.is_of_type('bam'):
+            #if str( $input.metadata.bam_index ) != "None":
+                    ln -s '${input.metadata.bam_index}' bamfile.bam.bai &&
             #else:
                     samtools index bamfile.bam bamfile.bai &&
             #end if
         #end if
 
-        java -jar $__tool_directory__/ScriptManager-v0.14.jar bam-format-converter bam-to-bed
+        java -jar $__tool_directory__/@JAR_FILENAME@ bam-format-converter bam-to-bed
 
+        #if str($gzip) == "Yes" :
+            --gzip
+        #end if
         #if str($read) == "read_1" :
             -1
         #else if str($read) == "read_2" :
@@ -27,62 +33,55 @@
         #else if str($read) == "fragment" :
             -f
         #end if
-
-        #if str($mate_pair) == "Yes" :
+        #if str($require_paired_end.mate_pair) == "Yes" :
             -p
+            #if str($require_paired_end.filter_by_min.filter_min) == "Yes" :
+                -n "$require_paired_end.filter_by_min.min_insert"
+            #end if
+            #if str($require_paired_end.filter_by_max.filter_max) == "Yes" :
+                -x "$require_paired_end.filter_by_max.max_insert"
+            #end if
         #end if
-
-        #if str($filter_by_min.filter_min) == "Yes" :
-            -n "$filter_by_min.min_insert"
-        #end if
-
-        -o output1.bed
-
-        #if str($filter_by_max.filter_max) == "Yes" :
-            -x "$filter_by_max.max_insert"
-        #end if
-
+        -o '$output'
         bamfile.bam
     ]]></command>
     <inputs>
-        <param type="data" name="BAM" format="bam" label="Input BAM file"/>
-
+        <param type="data" name="input" format="bam" label="Input BAM file"/>
         <param type="select" name="read" label="Select which read to output">
             <option value="read_1" selected="True" >Read 1</option>
             <option value="read_2" >Read 2</option>
             <option value="combined" >Combined </option>
             <option value="midpoint" >Midpoint (Require PE) </option>
             <option value="fragment" >Fragment (Require PE) </option>
         </param>
-
-        <param type="boolean" name="mate_pair" truevalue="Yes" falsevalue="No" label="Require proper mate-pair" />
-
-        <conditional name="filter_by_min">
-        <param type="boolean" name="filter_min" truevalue="Yes" falsevalue="No" label="Filter by min insert size (bp)" >
-            </param>
+        <conditional name="require_paired_end">
+            <param type="boolean" name="mate_pair" truevalue="Yes" falsevalue="No" label="Require proper mate-pair" />
             <when value="Yes">
-                <param type="integer" name="min_insert" value="0" label="Min insert size (bp)" />
-            </when>
-            <when value="No">
+              <conditional name="filter_by_min">
+                  <param type="boolean" name="filter_min" truevalue="Yes" falsevalue="No" label="Filter by min insert size (bp)" />
+                  <when value="Yes">
+                      <param type="integer" name="min_insert" value="0" label="Min insert size (bp)" />
+                  </when>
+                  <when value="No" />
+              </conditional>
+              <conditional name="filter_by_max">
+                  <param type="boolean" name="filter_max" truevalue="Yes" falsevalue="No" label="Filter by max insert size (bp)" />
+                  <when value="Yes">
+                      <param type="integer" name="max_insert" value="1000" label="Max insert size (bp)" />
+                  </when>
+                  <when value="No" />
+              </conditional>
             </when>
         </conditional>
-
-        <conditional name="filter_by_max">
-        <param type="boolean" name="filter_max" truevalue="Yes" falsevalue="No" label="Filter by max insert size (bp)" >
-        </param>
-            <when value="Yes">
-                <param type="integer" name="max_insert" value="1000" label="Max insert size (bp)" />
-            </when>
-            <when value="No">
-            </when>
-        </conditional>
-
+        <param name="gzip" type="boolean" checked="true" truevalue="Yes" falsevalue="No" label="Gzip output" />
     </inputs>
     <outputs>
-        <data name="output1" format="bed" label="${tool.name} (composite) on ${on_string}"/>
+        <data name="output" format="bed" label="${tool.name} (composite) on ${on_string}"/>
     </outputs>
     <help>
-    **What it does**
-    Convert BAM file to BED file.
+**What it does**
+
+Convert BAM file to BED file.
     </help>
-</tool>
+    <expand macro="citations_pearc" />
+</tool>