Mercurial > repos > bgruening > hicup_deduplicator

diff hicup_deduplicator.xml @ 4:46e5b4782715 draft

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planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit 22eec1b3b20b788e762837c02488f332f831fab3
author bgruening
date Fri, 25 May 2018 17:51:57 -0400
parents 6cc9a607f899
children a5934ac7c399
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--- a/hicup_deduplicator.xml	Thu Nov 09 11:15:26 2017 -0500
+++ b/hicup_deduplicator.xml	Fri May 25 17:51:57 2018 -0400
@@ -1,31 +1,35 @@
-<tool id="hicup_deduplicator" name="Hicup Deduplicator" version="@VERSION@.0">
+<tool id="hicup_deduplicator" name="Hicup Deduplicator" version="@VERSION@.0" profile="18.01">
     <description>removes duplicated di-tags (retaining one copy of each) from the data set.</description>
     <macros>
         <import>hicup_macros.xml</import>
     </macros>
     <expand macro="requirements_hicup" />
-    <expand macro="stdio" />
-
-    <command><![CDATA[
-        hicup_deduplicator --quiet '$input_file'
-        && mv *.dedup.* dataset.dedup_result
-        && mv hicup_deduplicator_summary*.txt hicup_deduplicator_summary.txt
-        && mv *deduplicator_cis_trans_piechart.svg deduplicator_cis_trans_piechart.svg
-        && mv *deduplicator_uniques_barchart.svg deduplicator_uniques_barchart.svg
+    <command detect_errors="exit_code"><![CDATA[
+        #if $input_file.ext != 'sam':
+            ln -s '$input_file' input.bam  &&
+        #end if
+        hicup_deduplicator --zip --quiet
+        #if $input_file.ext != 'sam':
+            input.bam
+        #else
+            '$input_file'
+        #end if
     ]]></command>
     <inputs>
-        <param name="input_file" type="data" format="bam,sam" label="Input file(s)" help="Input files in bam or sam format."/>
+        <param name="input_file" type="data" format="qname_sorted.bam,sam" label="Input file(s)" help="Input files in BAM or SAM format."/>
     </inputs>
     <outputs>
-       <data name="dedup_result" format="bam,sam" label="Deduplicator Result" from_work_dir="dataset.dedup_result" />
-       <expand macro="deduplicator_output" />
+        <data name="dedup_result" format="qname_sorted.bam" label="Deduplicator Result" from_work_dir="*dedup*.bam" />
+        <data name="cis_trans_piechart" format="svg" from_work_dir="*deduplicator_cis_trans_piechart.svg" label="Hicup Deduplicator Cis Trans Piechart.svg"/>
+        <data name="uniques_barchart" format="svg" from_work_dir="*deduplicator_uniques_barchart.svg" label="Hicup Deduplicator Uniques Barchart.svg" />
+        <data name="hicup_deduplicator_summary" format="txt" from_work_dir="hicup_deduplicator_summary*.txt" label="Hicup Deduplicator Summary" />
     </outputs>
     <tests>
         <test>
-            <param name="input_file" value="dataset.filt.sam" ftype="sam"/>
-            <output name="dataset_hicup" file="dataset.hicup.sam" lines_diff="5" />
-            <output name="cis_trans_piechart" file="deduplicator_cis_trans_piechart.svg" ftype="svg" lines_diff="1000"/>
-            <output name="uniques_barchart" file="deduplicator_uniques_barchart.svg" ftype="svg" lines_diff="1000"/>
+            <param name="input_file" value="dataset1_2.filt.bam" ftype="qname_sorted.bam"/>
+            <output name="dedup_result" file="dataset1_2.hicup.bam" lines_diff="5" ftype="qname_sorted.bam"/>
+            <output name="cis_trans_piechart" file="dataset1_2.filt.bam.deduplicator_cis_trans_piechart.svg" ftype="svg" lines_diff="1000"/>
+            <output name="uniques_barchart" file="dataset1_2.filt.bam.deduplicator_uniques_barchart.svg" ftype="svg" lines_diff="1000"/>
             <output name="hicup_deduplicator_summary" file="hicup_deduplicator_summary.txt" lines_diff="2"/>
         </test>
     </tests>