Mercurial > repos > drosofff > msp_sr_bowtie_parser

changeset 15:a39761c27e77 draft

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planemo upload for repository https://bitbucket.org/drosofff/gedtools/
author drosofff
date Mon, 29 Jun 2015 05:54:17 -0400
parents 115af29c4f57
children bfeaf4415eba
files sRbowtieParser.xml tool_dependencies.xml
diffstat 2 files changed, 2 insertions(+), 6 deletions(-) [+]
line wrap: on
line diff
--- a/sRbowtieParser.xml	Sun Jun 21 15:40:36 2015 -0400
+++ b/sRbowtieParser.xml	Mon Jun 29 05:54:17 2015 -0400
@@ -2,7 +2,6 @@
   <description></description>
   <requirements>
 	<requirement type="package" version="0.12.7">bowtie</requirement>
-        <requirement type="package" version="1.2">samtools</requirement>
         <requirement type="package" version="0.7.7">pysam</requirement>
         <requirement type="package" version="1.9">numpy</requirement>
  </requirements>
@@ -39,13 +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">
--- a/tool_dependencies.xml	Sun Jun 21 15:40:36 2015 -0400
+++ b/tool_dependencies.xml	Mon Jun 29 05:54:17 2015 -0400
@@ -3,9 +3,6 @@
   <package name="bowtie" version="0.12.7">
       <repository changeset_revision="f0faa5eea2eb" name="package_bowtie_0_12_7" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
-    <package name="samtools" version="1.2">
-      <repository changeset_revision="77e0e0891773" name="package_samtools_1_2" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-    </package>
     <package name="pysam" version="0.7.7">
       <repository changeset_revision="ca10c522f37e" name="package_pysam_0_7_7" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>