Mercurial > repos > devteam > samtools_idxstats
annotate samtools_idxstats.xml @ 1:88b8c2916784 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_idxstats commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
| author | iuc |
|---|---|
| date | Tue, 09 May 2017 11:19:02 -0400 |
| parents | 87398ae795c7 |
| children | 04d5581db1f5 |
| rev | line source |
|---|---|
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88b8c2916784
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_idxstats commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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1 <tool id="samtools_idxstats" name="IdxStats" version="2.0.1"> |
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88b8c2916784
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_idxstats commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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2 <description>reports stats of the BAM index file</description> |
| 0 | 3 <macros> |
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88b8c2916784
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_idxstats commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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4 <import>macros.xml</import> |
| 0 | 5 </macros> |
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88b8c2916784
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_idxstats commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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6 <expand macro="requirements"/> |
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88b8c2916784
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_idxstats commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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7 <expand macro="stdio"/> |
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88b8c2916784
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_idxstats commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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changeset
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8 <expand macro="version_command"/> |
| 0 | 9 <command><![CDATA[ |
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88b8c2916784
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_idxstats commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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10 ln -f -s '${input.metadata.bam_index}' '${input}.bai' && |
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88b8c2916784
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_idxstats commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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11 |
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88b8c2916784
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_idxstats commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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12 samtools idxstats '${input}' > '${output}' |
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88b8c2916784
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_idxstats commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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13 ]]></command> |
| 0 | 14 <inputs> |
| 15 <param name="input" type="data" format="bam" label="BAM file" /> | |
| 16 </inputs> | |
| 17 <outputs> | |
| 18 <data format="tabular" name="output" label="${tool.name} on ${on_string}" /> | |
| 19 </outputs> | |
| 20 <tests> | |
| 21 <test> | |
| 22 <param name="input" value="phiX.bam" ftype="bam" /> | |
| 23 <output name="output" file="samtools_idxstats_out.tabular" compare="diff" ftype="tabular" /> | |
| 24 </test> | |
| 25 </tests> | |
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88b8c2916784
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_idxstats commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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changeset
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26 <help><![CDATA[ |
| 0 | 27 **What it does** |
| 28 | |
| 29 Runs the ``samtools idxstats`` command. It retrieves and prints stats in the index file. | |
| 30 | |
| 31 Input is a sorted and indexed BAM file, the output is tabular with | |
| 32 four columns (one row per reference sequence plus a final line for | |
| 33 unmapped reads):: | |
| 34 | |
| 35 Column Description | |
| 36 ------ ----------------------------- | |
| 37 1 Reference sequence identifier | |
| 38 2 Reference sequence length | |
| 39 3 Number of mapped reads | |
| 40 4 Number of placed but unmapped reads | |
| 41 (typically unmapped partners of mapped reads) | |
| 42 | |
| 43 ------ | |
| 44 | |
| 45 **Example** output from a *de novo* assembly:: | |
| 46 | |
| 47 contig_1 170035 98397 0 | |
| 48 contig_2 403835 199564 0 | |
| 49 contig_3 553102 288189 0 | |
| 50 ... ... ... ... | |
| 51 contig_603 653 50 0 | |
| 52 contig_604 214 6 0 | |
| 53 \* 0 0 50320 | |
| 54 | |
| 55 In this example there were 604 contigs, each with one line in the output table, | |
| 56 plus the final row (labelled with an asterisk) representing 50320 unmapped reads. | |
| 57 In this BAM file, the final column was otherwise zero. | |
| 58 | |
| 59 ------ | |
| 60 | |
| 61 Peter J.A. Cock (2013), `Galaxy wrapper <https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats>`_ for the samtools idxstats command | |
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88b8c2916784
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_idxstats commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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62 ]]></help> |
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88b8c2916784
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_idxstats commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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changeset
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63 <expand macro="citations"/> |
| 0 | 64 </tool> |