Mercurial > repos > devteam > samtools_reheader
annotate samtools_reheader.xml @ 2:30388d878f81 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_reheader commit f667915d861dbf0a25cc8fd132cc956d82e73ee9"
author | iuc |
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date | Thu, 02 Jul 2020 05:25:02 -0400 |
parents | db000c6007a0 |
children | bb8cfc6f6e0c |
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30388d878f81
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_reheader commit f667915d861dbf0a25cc8fd132cc956d82e73ee9"
iuc
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1 <tool id="samtools_reheader" name="Reheader" version="2.0.1+galaxy1"> |
0 | 2 <description>copy SAM/BAM header between datasets</description> |
3 <macros> | |
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db000c6007a0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_reheader commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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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
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5 </macros> |
db000c6007a0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_reheader commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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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
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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
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0
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changeset
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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
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9 <command><![CDATA[ |
db000c6007a0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_reheader commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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10 samtools reheader |
db000c6007a0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_reheader commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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11 '${input_header}' |
db000c6007a0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_reheader commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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changeset
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12 '${input_file}' |
2
30388d878f81
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_reheader commit f667915d861dbf0a25cc8fd132cc956d82e73ee9"
iuc
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13 ${no_pg} |
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db000c6007a0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_reheader commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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14 > '${output}' |
db000c6007a0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_reheader commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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15 ]]></command> |
0 | 16 <inputs> |
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."/> | |
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."/> | |
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30388d878f81
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_reheader commit f667915d861dbf0a25cc8fd132cc956d82e73ee9"
iuc
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changeset
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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
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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
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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 | 22 </inputs> |
23 <outputs> | |
24 <data format="bam" name="output" label="${tool.name} on ${on_string}" /> | |
25 </outputs> | |
26 <tests> | |
27 <test> | |
28 <param name="input_header" ftype="bam" value="reheader_input_header.bam"/> | |
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
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30 <output name="output" ftype="bam" file="reheader_out.bam" lines_diff="1"/><!-- samtools adds reheader line --> |
0 | 31 </test> |
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30388d878f81
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_reheader commit f667915d861dbf0a25cc8fd132cc956d82e73ee9"
iuc
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1
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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
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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
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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
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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
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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
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37 </test> |
0 | 38 </tests> |
39 <help> | |
40 **What it does** | |
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
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42 Generates a new BAM dataset with the contents of *target* dataset, but the header of *source* dataset using the ``samtools reheader`` command. |
0 | 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
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44 <expand macro="citations"/> |
0 | 45 </tool> |
46 |