Mercurial > repos > devteam > samtools_split

annotate samtools_split.xml @ 5:bd850490c7f1 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-iuc/tree/master/tool_collections/samtools/samtools_split commit cd62639660bef041ba14ecff337fb98e84e75d8a
author iuc
date Mon, 20 Nov 2023 22:16:50 +0000
parents bcedabb53ddf
children 818030fa6bbf
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
5
bd850490c7f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_split commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents: 4
diff changeset
1 <tool id="samtools_split" name="Samtools split" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
0
57f3e32f809d Uploaded
devteam
parents:
diff changeset
2 <description>BAM dataset on readgroups</description>
57f3e32f809d Uploaded
devteam
parents:
diff changeset
3 <macros>
57f3e32f809d Uploaded
devteam
parents:
diff changeset
4 <import>macros.xml</import>
57f3e32f809d Uploaded
devteam
parents:
diff changeset
5 </macros>
1
b7f7826ef1cd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_split commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents: 0
diff changeset
6 <expand macro="requirements"/>
b7f7826ef1cd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_split commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents: 0
diff changeset
7 <expand macro="stdio"/>
b7f7826ef1cd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_split commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents: 0
diff changeset
8 <expand macro="version_command"/>
0
57f3e32f809d Uploaded
devteam
parents:
diff changeset
9 <command><![CDATA[
2
135c85f4cfaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_split commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents: 1
diff changeset
10 @ADDTHREADS@
135c85f4cfaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_split commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents: 1
diff changeset
11 samtools split -f 'Read_Group_%!.bam'
135c85f4cfaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_split commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents: 1
diff changeset
12 #if $header:
135c85f4cfaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_split commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents: 1
diff changeset
13 -u '${output}:${header}'
135c85f4cfaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_split commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents: 1
diff changeset
14 #else:
135c85f4cfaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_split commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents: 1
diff changeset
15 -u '${output}'
135c85f4cfaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_split commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents: 1
diff changeset
16 #end if
135c85f4cfaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_split commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents: 1
diff changeset
17 -@ \$addthreads
135c85f4cfaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_split commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents: 1
diff changeset
18 '$input_bam'
1
b7f7826ef1cd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_split commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents: 0
diff changeset
19 ]]></command>
0
57f3e32f809d Uploaded
devteam
parents:
diff changeset
20 <inputs>
57f3e32f809d Uploaded
devteam
parents:
diff changeset
21 <param name="input_bam" type="data" format="bam" label="BAM file" />
1
b7f7826ef1cd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_split commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents: 0
diff changeset
22 <param name="header" type="data" format="bam,sam" optional="True" label="Replace header in output file" />
0
57f3e32f809d Uploaded
devteam
parents:
diff changeset
23 </inputs>
57f3e32f809d Uploaded
devteam
parents:
diff changeset
24 <outputs>
1
b7f7826ef1cd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_split commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents: 0
diff changeset
25 <data name="output" format="bam" label="${tool.name} on ${on_string}">
2
135c85f4cfaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_split commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents: 1
diff changeset
26 <discover_datasets pattern="Read_Group_(?P&lt;designation&gt;.+)\.bam" ext="bam" visible="true" directory="" assign_primary_output="false"/>
0
57f3e32f809d Uploaded
devteam
parents:
diff changeset
27 </data>
57f3e32f809d Uploaded
devteam
parents:
diff changeset
28 </outputs>
57f3e32f809d Uploaded
devteam
parents:
diff changeset
29 <tests>
57f3e32f809d Uploaded
devteam
parents:
diff changeset
30 <test>
57f3e32f809d Uploaded
devteam
parents:
diff changeset
31 <param name="input_bam" value="phiX.bam" ftype="bam" />
2
135c85f4cfaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_split commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents: 1
diff changeset
32 <output name="output">
3
5d9ae78f34d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_split commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 2
diff changeset
33 <discovered_dataset designation="Mouse" ftype="bam" file="phiX_Mouse.bam" lines_diff="4" />
5d9ae78f34d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_split commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 2
diff changeset
34 <discovered_dataset designation="Elephant" ftype="bam" file="phiX_Elephant.bam" lines_diff="4" />
5d9ae78f34d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_split commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 2
diff changeset
35 <discovered_dataset designation="Human" ftype="bam" file="phiX_Human.bam" lines_diff="4" />
0
57f3e32f809d Uploaded
devteam
parents:
diff changeset
36 </output>
57f3e32f809d Uploaded
devteam
parents:
diff changeset
37 </test>
57f3e32f809d Uploaded
devteam
parents:
diff changeset
38 </tests>
1
b7f7826ef1cd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_split commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents: 0
diff changeset
39 <help><![CDATA[
0
57f3e32f809d Uploaded
devteam
parents:
diff changeset
40 **What it does**
57f3e32f809d Uploaded
devteam
parents:
diff changeset
41
57f3e32f809d Uploaded
devteam
parents:
diff changeset
42 Splits BAM files on readgroups.
57f3e32f809d Uploaded
devteam
parents:
diff changeset
43
1
b7f7826ef1cd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_split commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents: 0
diff changeset
44 This tool is based on ``samtools split`` command. It will generate multiple output datasets for each redagroup from the input dataset.
b7f7826ef1cd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_split commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents: 0
diff changeset
45 ]]></help>
b7f7826ef1cd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_split commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents: 0
diff changeset
46 <expand macro="citations"/>
0
57f3e32f809d Uploaded
devteam
parents:
diff changeset
47 </tool>