Mercurial > repos > devteam > samtools_reheader

annotate samtools_reheader.xml @ 3:b5e69833722f draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/samtools/samtools_reheader commit de7140295cce07e1bc1697e51dab4271c8d7a8a6
author devteam
date Fri, 18 Dec 2015 19:45:43 -0500
parents 77a6694ebf7a
children 0b97d4e945ab
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
2
77a6694ebf7a planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 0
diff changeset
1 <tool id="samtools_reheader" name="Reheader" version="2.0">
77a6694ebf7a planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 0
diff changeset
2 <description>copy SAM/BAM header between datasets</description>
77a6694ebf7a planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 0
diff changeset
3 <macros>
77a6694ebf7a planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 0
diff changeset
4 <import>macros.xml</import>
77a6694ebf7a planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 0
diff changeset
5 </macros>
77a6694ebf7a planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 0
diff changeset
6 <expand macro="requirements"></expand>
77a6694ebf7a planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 0
diff changeset
7 <expand macro="stdio"></expand>
77a6694ebf7a planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 0
diff changeset
8 <expand macro="version_command"></expand>
0
c50efc142ad0 Uploaded initial tool definition.
devteam
parents:
diff changeset
9 <command><![CDATA[samtools reheader "${input_header}" "${input_file}" > "${output}"]]></command>
c50efc142ad0 Uploaded initial tool definition.
devteam
parents:
diff changeset
10 <inputs>
2
77a6694ebf7a planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 0
diff changeset
11 <param name="input_header" type="data" format="sam,bam" label="Select source dataset" help="Header from this dataset will be used to replace header in the target dataset. May be either SAM or BAM dataset."/>
77a6694ebf7a planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 0
diff changeset
12 <param name="input_file" type="data" format="bam" label="Select target dataset" help="Header from the source dataset will be inserted here. Should be a BAM dataset."/>
0
c50efc142ad0 Uploaded initial tool definition.
devteam
parents:
diff changeset
13 </inputs>
c50efc142ad0 Uploaded initial tool definition.
devteam
parents:
diff changeset
14 <outputs>
c50efc142ad0 Uploaded initial tool definition.
devteam
parents:
diff changeset
15 <data format="bam" name="output" label="${tool.name} on ${on_string}" />
c50efc142ad0 Uploaded initial tool definition.
devteam
parents:
diff changeset
16 </outputs>
c50efc142ad0 Uploaded initial tool definition.
devteam
parents:
diff changeset
17 <tests>
2
77a6694ebf7a planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 0
diff changeset
18 <test>
77a6694ebf7a planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 0
diff changeset
19 <param name="input_header" ftype="bam" value="reheader_input_header.bam"/>
77a6694ebf7a planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 0
diff changeset
20 <param name="input_file" ftype="bam" value="reheader_input_file.bam"/>
77a6694ebf7a planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 0
diff changeset
21 <output name="output" ftype="bam" file="reheader_out.bam"/>
77a6694ebf7a planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 0
diff changeset
22 </test>
0
c50efc142ad0 Uploaded initial tool definition.
devteam
parents:
diff changeset
23 </tests>
c50efc142ad0 Uploaded initial tool definition.
devteam
parents:
diff changeset
24 <help>
c50efc142ad0 Uploaded initial tool definition.
devteam
parents:
diff changeset
25 **What it does**
c50efc142ad0 Uploaded initial tool definition.
devteam
parents:
diff changeset
26
2
77a6694ebf7a planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 0
diff changeset
27 Copies header from *source* dataset into *target* dataset using ``samtools reheader`` command.
0
c50efc142ad0 Uploaded initial tool definition.
devteam
parents:
diff changeset
28
c50efc142ad0 Uploaded initial tool definition.
devteam
parents:
diff changeset
29 </help>
2
77a6694ebf7a planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 0
diff changeset
30 <expand macro="citations"></expand>
0
c50efc142ad0 Uploaded initial tool definition.
devteam
parents:
diff changeset
31 </tool>
c50efc142ad0 Uploaded initial tool definition.
devteam
parents:
diff changeset
32