annotate samtools_reheader.xml @ 5:85e38b31e8b3 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_reheader commit 9c5a35ce695c3d134e41d8695487edd5f71ea33c
author iuc
date Sun, 08 Sep 2024 03:26:29 +0000
parents d7b4851d1971
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
4
d7b4851d1971 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_reheader commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents: 3
diff changeset
1 <tool id="samtools_reheader" name="Samtools reheader" version="2.0.3" profile="@PROFILE@">
0
020e144b5f78 Uploaded
devteam
parents:
diff changeset
2 <description>copy SAM/BAM header between datasets</description>
020e144b5f78 Uploaded
devteam
parents:
diff changeset
3 <macros>
1
db000c6007a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_reheader commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents: 0
diff changeset
4 <import>macros.xml</import>
db000c6007a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_reheader commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents: 0
diff changeset
5 </macros>
db000c6007a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_reheader commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents: 0
diff changeset
6 <expand macro="requirements"/>
db000c6007a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_reheader commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents: 0
diff changeset
7 <expand macro="stdio"/>
db000c6007a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_reheader commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents: 0
diff changeset
8 <expand macro="version_command"/>
db000c6007a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_reheader commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents: 0
diff changeset
9 <command><![CDATA[
db000c6007a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_reheader commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents: 0
diff changeset
10 samtools reheader
db000c6007a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_reheader commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents: 0
diff changeset
11 '${input_header}'
db000c6007a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_reheader commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents: 0
diff changeset
12 '${input_file}'
2
30388d878f81 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_reheader commit f667915d861dbf0a25cc8fd132cc956d82e73ee9"
iuc
parents: 1
diff changeset
13 ${no_pg}
1
db000c6007a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_reheader commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents: 0
diff changeset
14 > '${output}'
db000c6007a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_reheader commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents: 0
diff changeset
15 ]]></command>
0
020e144b5f78 Uploaded
devteam
parents:
diff changeset
16 <inputs>
020e144b5f78 Uploaded
devteam
parents:
diff changeset
17 <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."/>
020e144b5f78 Uploaded
devteam
parents:
diff changeset
18 <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."/>
2
30388d878f81 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_reheader commit f667915d861dbf0a25cc8fd132cc956d82e73ee9"
iuc
parents: 1
diff changeset
19 <param argument="--no-PG" name="no_pg" type="boolean" truevalue="--no-PG" falsevalue=""
30388d878f81 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_reheader commit f667915d861dbf0a25cc8fd132cc956d82e73ee9"
iuc
parents: 1
diff changeset
20 label="Keep the new header unmodified?"
30388d878f81 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_reheader commit f667915d861dbf0a25cc8fd132cc956d82e73ee9"
iuc
parents: 1
diff changeset
21 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." />
0
020e144b5f78 Uploaded
devteam
parents:
diff changeset
22 </inputs>
020e144b5f78 Uploaded
devteam
parents:
diff changeset
23 <outputs>
020e144b5f78 Uploaded
devteam
parents:
diff changeset
24 <data format="bam" name="output" label="${tool.name} on ${on_string}" />
020e144b5f78 Uploaded
devteam
parents:
diff changeset
25 </outputs>
020e144b5f78 Uploaded
devteam
parents:
diff changeset
26 <tests>
020e144b5f78 Uploaded
devteam
parents:
diff changeset
27 <test>
020e144b5f78 Uploaded
devteam
parents:
diff changeset
28 <param name="input_header" ftype="bam" value="reheader_input_header.bam"/>
020e144b5f78 Uploaded
devteam
parents:
diff changeset
29 <param name="input_file" ftype="bam" value="reheader_input_file.bam"/>
1
db000c6007a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_reheader commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents: 0
diff changeset
30 <output name="output" ftype="bam" file="reheader_out.bam" lines_diff="1"/><!-- samtools adds reheader line -->
0
020e144b5f78 Uploaded
devteam
parents:
diff changeset
31 </test>
2
30388d878f81 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_reheader commit f667915d861dbf0a25cc8fd132cc956d82e73ee9"
iuc
parents: 1
diff changeset
32 <test>
30388d878f81 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_reheader commit f667915d861dbf0a25cc8fd132cc956d82e73ee9"
iuc
parents: 1
diff changeset
33 <param name="input_header" ftype="bam" value="reheader_input_header.bam"/>
30388d878f81 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_reheader commit f667915d861dbf0a25cc8fd132cc956d82e73ee9"
iuc
parents: 1
diff changeset
34 <param name="input_file" ftype="bam" value="reheader_input_file.bam"/>
30388d878f81 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_reheader commit f667915d861dbf0a25cc8fd132cc956d82e73ee9"
iuc
parents: 1
diff changeset
35 <param name="no_pg" value="true"/>
30388d878f81 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_reheader commit f667915d861dbf0a25cc8fd132cc956d82e73ee9"
iuc
parents: 1
diff changeset
36 <output name="output" ftype="bam" file="reheader_out.bam" />
30388d878f81 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_reheader commit f667915d861dbf0a25cc8fd132cc956d82e73ee9"
iuc
parents: 1
diff changeset
37 </test>
0
020e144b5f78 Uploaded
devteam
parents:
diff changeset
38 </tests>
020e144b5f78 Uploaded
devteam
parents:
diff changeset
39 <help>
020e144b5f78 Uploaded
devteam
parents:
diff changeset
40 **What it does**
020e144b5f78 Uploaded
devteam
parents:
diff changeset
41
2
30388d878f81 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_reheader commit f667915d861dbf0a25cc8fd132cc956d82e73ee9"
iuc
parents: 1
diff changeset
42 Generates a new BAM dataset with the contents of *target* dataset, but the header of *source* dataset using the ``samtools reheader`` command.
0
020e144b5f78 Uploaded
devteam
parents:
diff changeset
43 </help>
1
db000c6007a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_reheader commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents: 0
diff changeset
44 <expand macro="citations"/>
0
020e144b5f78 Uploaded
devteam
parents:
diff changeset
45 </tool>