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changeset 1:a8b94864fe35 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gatk/print_reads commit a1517c9d22029095120643bbe2c8fa53754dd2b7
author devteam
date Wed, 11 Nov 2015 12:44:29 -0500
parents e768f4851646
children
files print_reads.xml tool_dependencies.xml
diffstat 2 files changed, 4 insertions(+), 13 deletions(-) [+]
line wrap: on
line diff
--- a/print_reads.xml	Tue Apr 01 10:48:38 2014 -0400
+++ b/print_reads.xml	Wed Nov 11 12:44:29 2015 -0500
@@ -1,4 +1,4 @@
-<tool id="gatk_print_reads" name="Print Reads" version="0.0.1">
+<tool id="gatk_print_reads" name="Print Reads" version="0.0.2">
   <description>from BAM files</description>
   <requirements>
       <requirement type="package" version="1.4">gatk</requirement>
@@ -73,7 +73,7 @@
     <param name="platform" type="text" value="" label="Exclude all reads with this platform from the output" help="-platform,--platform &amp;lt;platform&amp;gt;" />
     <param name="read_group" type="text" value="" label="Exclude all reads with this read group from the output" help="-readGroup,--readGroup &amp;lt;readGroup&amp;gt;" />
     <repeat name="sample_file_repeat" title="File containing a list of samples to include" help="-sf,--sample_file &amp;lt;sample_file&amp;gt;">
-        <param name="input_sample_file" type="data" format="text" label="Sample file" />
+        <param name="input_sample_file" type="data" format="txt" label="Sample file" />
     </repeat>
     <repeat name="sample_name_repeat" title="Sample name to be included in the analysis" help="-sn,--sample_name &amp;lt;sample_name&amp;gt;">
         <param name="sample_name" type="text" label="Sample name" />
@@ -86,15 +86,6 @@
     <data format="bam" name="output_bam" label="${tool.name} on ${on_string} (BAM)" />
     <data format="txt" name="output_log" label="${tool.name} on ${on_string} (log)" />
   </outputs>
-    <param name="number" type="integer" value="-1" label="Print the first n reads from the file, discarding the rest" />
-    <param name="platform" type="text" value="" label="Exclude all reads with this platform from the output" />
-    <param name="read_group" type="text" value="" label="Exclude all reads with this read group from the output" />
-    <repeat name="sample_file_repeat" title="File containing a list of samples to include">
-        <param name="input_sample_file" type="data" format="text" label="Sample file" />
-    </repeat>
-    <repeat name="sample_name_repeat" title="Sample name to be included in the analysis">
-        <param name="sample_name" type="text" label="Sample name" />
-    </repeat>
   <tests>
       <test>
           <param name="reference_source_selector" value="history" />
--- a/tool_dependencies.xml	Tue Apr 01 10:48:38 2014 -0400
+++ b/tool_dependencies.xml	Wed Nov 11 12:44:29 2015 -0500
@@ -1,9 +1,9 @@
 <?xml version="1.0"?>
 <tool_dependency>
   <package name="gatk" version="1.4">
-      <repository changeset_revision="ec95ec570854" name="package_gatk_1_4" owner="devteam" prior_installation_required="False" toolshed="http://toolshed.g2.bx.psu.edu" />
+      <repository changeset_revision="ec95ec570854" name="package_gatk_1_4" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
     <package name="samtools" version="0.1.18">
-      <repository changeset_revision="171cd8bc208d" name="package_samtools_0_1_18" owner="devteam" prior_installation_required="False" toolshed="http://toolshed.g2.bx.psu.edu" />
+      <repository changeset_revision="171cd8bc208d" name="package_samtools_0_1_18" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>