diff samtools_reheader.xml @ 6:747cd1b9ae98 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_reheader commit f667915d861dbf0a25cc8fd132cc956d82e73ee9"

--- a/samtools_reheader.xml	Sun Jul 28 14:49:41 2019 -0400
+++ b/samtools_reheader.xml	Mon Jul 06 18:13:42 2020 +0000
@@ -1,4 +1,4 @@
-<tool id="samtools_reheader" name="Reheader" version="2.0.1">
+<tool id="samtools_reheader" name="Reheader" version="2.0.1+galaxy1">
     <description>copy SAM/BAM header between datasets</description>
     <macros>
         <import>macros.xml</import>
@@ -10,11 +10,15 @@
         samtools reheader
             '${input_header}'
             '${input_file}'
+            ${no_pg}
             > '${output}'
     ]]></command>
     <inputs>
         <param name="input_header" type="data" format="sam,bam" label="Select source dataset" help="Header from this dataset will be used to replace header in the target dataset. May be either SAM or BAM dataset."/>
         <param name="input_file" type="data" format="bam" label="Select target dataset" help="Header from the source dataset will be inserted here. Should be a BAM dataset."/>
+        <param argument="--no-PG" name="no_pg" type="boolean" truevalue="--no-PG" falsevalue=""
+        label="Keep the new header unmodified?"
+        help="By default, samtools reheader will add itself to the chain of tools used to manipulate the target dataset, which will cause one or more @PG records to be inserted into the new header. If you want the output dataset to end up with the header of the source dataset exactly, you should activate this option." />
     </inputs>
     <outputs>
         <data format="bam" name="output" label="${tool.name} on ${on_string}" />
@@ -25,11 +29,17 @@
             <param name="input_file" ftype="bam" value="reheader_input_file.bam"/>
             <output name="output" ftype="bam" file="reheader_out.bam" lines_diff="1"/><!-- samtools adds reheader line -->
         </test>
+        <test>
+            <param name="input_header" ftype="bam" value="reheader_input_header.bam"/>
+            <param name="input_file" ftype="bam" value="reheader_input_file.bam"/>
+            <param name="no_pg" value="true"/>
+            <output name="output" ftype="bam" file="reheader_out.bam" />
+        </test>
     </tests>
     <help>
 **What it does**
 
-Copies header from *source* dataset into *target* dataset using ``samtools reheader`` command.
+Generates a new BAM dataset with the contents of *target* dataset, but the header of *source* dataset using the ``samtools reheader`` command.
     </help>
     <expand macro="citations"/>
 </tool>