Mercurial > repos > drosofff > msp_sr_readmap_and_size_histograms

changeset 4:dffa22efc6a8 draft

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planemo upload for repository https://bitbucket.org/drosofff/gedtools/
author drosofff
date Mon, 29 Jun 2015 05:54:47 -0400
parents f6dc63230483
children 6ee5a6e89aa4
files readmap.xml tool_dependencies.xml
diffstat 2 files changed, 3 insertions(+), 7 deletions(-) [+]
line wrap: on
line diff
--- a/readmap.xml	Sun Jun 21 16:50:56 2015 -0400
+++ b/readmap.xml	Mon Jun 29 05:54:47 2015 -0400
@@ -2,7 +2,6 @@
   <description>from sRbowtie aligment</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="2.14">biocbasics</requirement>
         <requirement type="package" version="1.9">numpy</requirement>
@@ -57,7 +56,7 @@
            </param>
            <when value="indexed">
 	     <repeat name="series" title="Add alignment files">
-	       <param name="input" type="data" label="Select multiple alignments to parse">
+	       <param name="input" type="data" label="Select multiple alignments to parse" format="tabular,sam,bam">
                   <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>
 	       <param name="norm" type="float" value="1" label="Indicate a normalization factor to compare multiple aligments"/>
@@ -66,7 +65,7 @@
            <when value="history">
              <param name="ownFile" type="data" format="fasta" label="Select a fasta file, that served as the reference index for the alignments" />
 	     <repeat name="series" title="Add alignment files">
-	       <param name="input" type="data" label="Select multiple alignments to parse"/>
+	       <param name="input" type="data" label="Select multiple alignments to parse" format="tabular,sam,bam"/>
 	       <param name="norm" type="float" value="1" label="Indicate a normalization factor to compare multiple aligments"/>
 	     </repeat>
 	   </when>
--- a/tool_dependencies.xml	Sun Jun 21 16:50:56 2015 -0400
+++ b/tool_dependencies.xml	Mon Jun 29 05:54:47 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="0.1.18">
-      <repository changeset_revision="c0f72bdba484" name="package_samtools_0_1_18" owner="devteam" 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>
@@ -13,6 +10,6 @@
         <repository changeset_revision="43cb426cb05d" name="package_numpy_1_9" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
     <package name="biocbasics" version="2.14">
-        <repository changeset_revision="cd2113c820f7" name="package_biocbasics" owner="mvdbeek" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="565bfe059907" name="package_biocbasics" owner="mvdbeek" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>