diff bellerophon.xml @ 0:eca6296a091a draft

"planemo upload for repository https://github.com/davebx/bellerophon commit 5fe46c36adac4843cd548802073aa62b0afc61cd"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bellerophon.xml	Fri May 28 20:54:47 2021 +0000
@@ -0,0 +1,64 @@
+<tool id="bellerophon" name="Filter and merge" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
+    <description>chimeric reads from Arima Genomics</description>
+    <macros>
+        <token name="@TOOL_VERSION@">1.0</token>
+        <token name="@VERSION_SUFFIX@">0</token>
+    </macros>
+    <requirements>
+        <requirement type="package" version="@TOOL_VERSION@">bellerophon</requirement>
+        <requirement type="package" version="1.12">samtools</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        #if $forward.is_of_type("sam"):
+            #set $forward_input = 'forward_input.sam'
+            ln -s '${forward}' '$forward_input' &&
+        #else:
+            #set $forward_input = 'forward_input.bam'
+            ln -s '${forward}' '$forward_input' &&
+        #end if
+        #if $reverse.is_of_type("sam"):
+            #set $reverse_input = 'reverse_input.sam'
+            ln -s '${reverse}' '$reverse_input' &&
+        #else: 
+            #set $reverse_input = 'reverse_input.bam'
+            ln -s '${reverse}' '$reverse_input' &&
+        #end if
+        bellerophon
+        --forward $forward_input
+        --reverse $reverse_input
+        --quality $quality
+        --output 'merged_out.bam'
+        && samtools sort --no-PG -O BAM -o '$outfile' -@ \${GALAXY_SLOTS:-1} merged_out.bam
+        ]]>
+    </command>
+    <inputs>
+        <param argument="--forward" type="data" format="qname_sorted.bam,sam" label="First set of reads"
+            help="This is usually the forward reads in your experiment." />
+        <param argument="--reverse" type="data" format="qname_sorted.bam,sam" label="Second set of reads"
+            help="This is usually the reverse reads in your experiment." />
+        <param argument="--quality" type="integer" value="20" label="Minimum mapping quality"/>
+    </inputs>
+    <outputs>
+        <data name="outfile" format="bam"/>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="forward" value="forward.bam" ftype="qname_sorted.bam" />
+            <param name="reverse" value="reverse.bam" ftype="qname_sorted.bam" />
+            <param name="quality" value="20" />
+            <output name="outfile" file="merged-out.bam" ftype="bam" />
+        </test>
+        <test expect_num_outputs="1">
+            <param name="forward" value="forward.sam" ftype="sam" />
+            <param name="reverse" value="reverse.sam" ftype="sam" />
+            <param name="quality" value="12" />
+            <output name="outfile" file="merged-sam.bam" ftype="bam" />
+        </test>
+    </tests>
+    <help><![CDATA[
+        Filter mapped reads where the mapping spans a junction, retaining the 5-prime read. This is usually needed when dealing with data from Arima Genomics.
+    ]]></help>
+    <citations>
+        <citation type="doi">10.1038/s41586-021-03451-0</citation>
+    </citations>
+</tool>