Mercurial > repos > drosofff > msp_sr_bowtie_parser

diff sRbowtieParser.xml @ 1:ca3845fb0b31 draft default tip

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie_parser commit 70312b58ba246c07e70cdbd0a097f274f1386d09
author drosofff
date Mon, 18 Apr 2016 10:09:08 -0400
parents b996480cd604
children
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--- a/sRbowtieParser.xml	Wed May 27 17:19:15 2015 -0400
+++ b/sRbowtieParser.xml	Mon Apr 18 10:09:08 2016 -0400
@@ -1,14 +1,12 @@
-<tool id="sRbowtieParser" name="Parse items in sRbowtie alignment" version="1.0.1">
+<tool id="sRbowtieParser" name="Parse items in sRbowtie alignment" version="1.0.6">
   <description></description>
   <requirements>
 	<requirement type="package" version="0.12.7">bowtie</requirement>
-        <requirement type="package" version="0.1.18">samtools</requirement>
         <requirement type="package" version="0.7.7">pysam</requirement>
         <requirement type="package" version="1.9">numpy</requirement>
-        <requirement type="package" version="0.14">scipy</requirement>
  </requirements>
-<command interpreter="python">
-        sRbowtieParser.py 
+<command>
+        python $__tool_directory__/sRbowtieParser.py
 	          #if $refGenomeSource.genomeSource == "history":
                     --IndexSource $refGenomeSource.ownFile
          	    --ExtractDirective fastaSource
@@ -29,7 +27,7 @@
                   #end for
                   --alignmentLabel          
                   #for $i in $refGenomeSource.input_list
-                    "$i.name"
+                    "$i.element_identifier"
                   #end for
 
 </command>
@@ -40,13 +38,13 @@
                <option value="history">Use one from the history</option>
            </param>
            <when value="indexed">
-               <param name="input_list" type="data" label="Select multiple alignments to parse" multiple="true">
+               <param name="input_list" type="data" format="tabular,sam,bam" label="Select multiple alignments to parse" multiple="true">
                   <validator type="dataset_metadata_in_data_table" table_name="bowtie_indexes" metadata_name="dbkey" metadata_column="0" message="database not set for this bowtie output. Select the database(=genome used for matching) manually, or select a reference fasta from your history."/>
                </param>
            </when>
            <when value="history">
                 <param name="ownFile" type="data" format="fasta"  label="Select the fasta reference" />
-	        <param name="input_list" type="data" label="Select multiple alignments to parse" multiple="true"/>
+	        <param name="input_list" type="data" format="tabular,sam,bam" label="Select multiple alignments to parse" multiple="true"/>
            </when>
        </conditional>  <!-- refGenomeSource -->
        <param name="polarity" type="select" label="how to count sense and antisense reads">