Mercurial > repos > devteam > samtools_split
annotate samtools_split.xml @ 6:818030fa6bbf draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_split commit 9c5a35ce695c3d134e41d8695487edd5f71ea33c
author | iuc |
---|---|
date | Sun, 08 Sep 2024 03:26:49 +0000 |
parents | bd850490c7f1 |
children |
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 | 2 <description>BAM dataset on readgroups</description> |
3 <macros> | |
4 <import>macros.xml</import> | |
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 | 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@ |
6
818030fa6bbf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_split commit 9c5a35ce695c3d134e41d8695487edd5f71ea33c
iuc
parents:
5
diff
changeset
|
11 samtools split -f 'Read_Group_%!.bam' --output-fmt '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
|
12 #if $header: |
6
818030fa6bbf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_split commit 9c5a35ce695c3d134e41d8695487edd5f71ea33c
iuc
parents:
5
diff
changeset
|
13 -h $header' |
2
135c85f4cfaf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_split commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents:
1
diff
changeset
|
14 #end if |
6
818030fa6bbf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_split commit 9c5a35ce695c3d134e41d8695487edd5f71ea33c
iuc
parents:
5
diff
changeset
|
15 -u '$output' |
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
|
16 -@ \$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
|
17 '$input_bam' |
1
b7f7826ef1cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_split commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
0
diff
changeset
|
18 ]]></command> |
0 | 19 <inputs> |
20 <param name="input_bam" type="data" format="bam" label="BAM file" /> | |
1
b7f7826ef1cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_split commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
0
diff
changeset
|
21 <param name="header" type="data" format="bam,sam" optional="True" label="Replace header in output file" /> |
0 | 22 </inputs> |
23 <outputs> | |
1
b7f7826ef1cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_split commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
0
diff
changeset
|
24 <data name="output" format="bam" label="${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
|
25 <discover_datasets pattern="Read_Group_(?P<designation>.+)\.bam" ext="bam" visible="true" directory="" assign_primary_output="false"/> |
0 | 26 </data> |
27 </outputs> | |
28 <tests> | |
29 <test> | |
30 <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
|
31 <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
|
32 <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
|
33 <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
|
34 <discovered_dataset designation="Human" ftype="bam" file="phiX_Human.bam" lines_diff="4" /> |
0 | 35 </output> |
36 </test> | |
37 </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
|
38 <help><![CDATA[ |
0 | 39 **What it does** |
40 | |
41 Splits BAM files on readgroups. | |
42 | |
6
818030fa6bbf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_split commit 9c5a35ce695c3d134e41d8695487edd5f71ea33c
iuc
parents:
5
diff
changeset
|
43 This tool is based on ``samtools split`` command. It will generate multiple output datasets for each readgroup from the input dataset. |
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 ]]></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
|
45 <expand macro="citations"/> |
0 | 46 </tool> |