Mercurial > repos > iuc > bedtools
annotate multiCov.xml @ 46:64e2edfe7a2c draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 3e7bf5ae62de3520635d75e3825701960b9722e4
author | iuc |
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date | Sat, 18 May 2024 23:28:38 +0000 |
parents | 7ab85ac5f64b |
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3e38c9b3214f
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 1e25e8d0bd1ebeb2b94c4bbdff222e56defc1fc2"
iuc
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1 <tool id="bedtools_multicovtbed" name="bedtools MultiCovBed" version="@TOOL_VERSION@" profile="@PROFILE@"> |
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607c0576c6ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 6692e3a4fa1bf6e9a407735afdbb2454ed32b316
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2 <description>counts coverage from multiple BAMs at specific intervals</description> |
0 | 3 <macros> |
4 <import>macros.xml</import> | |
5 </macros> | |
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7ab85ac5f64b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 500a03281ea704abc7a16d9af63d67dbdcc5cd0b"
iuc
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6 <expand macro="bio_tools" /> |
0 | 7 <expand macro="requirements" /> |
8 <expand macro="stdio" /> | |
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dde39ba9c031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
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9 <command><![CDATA[ |
dde39ba9c031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
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10 #for $i, $bam in enumerate($bams): |
dde39ba9c031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
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11 ln -s -f '$bam' ${i}.bam && |
dde39ba9c031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
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12 ln -s -f '$bam.metadata.bam_index' ${i}.bam.bai && |
dde39ba9c031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
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13 #end for |
1 | 14 |
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dde39ba9c031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
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15 bedtools multicov |
dde39ba9c031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
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16 -bed '$input' |
dde39ba9c031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
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17 -bams |
dde39ba9c031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents:
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18 #for $i, $bam in enumerate($bams): |
dde39ba9c031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
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19 '${i}.bam' |
dde39ba9c031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
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20 #end for |
dde39ba9c031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
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21 $strand |
dde39ba9c031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
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22 @OVERLAP@ |
dde39ba9c031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
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23 $reciprocal |
dde39ba9c031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
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24 $split |
dde39ba9c031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
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25 -q $q |
dde39ba9c031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
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26 $duplicate |
dde39ba9c031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
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27 $failed |
dde39ba9c031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
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28 $proper |
dde39ba9c031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
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29 > '$output' |
dde39ba9c031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
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30 ]]></command> |
0 | 31 <inputs> |
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dde39ba9c031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
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32 <param name="input" argument="-bed" type="data" format="@STD_BEDTOOLS_INPUTS@" label="Sorted @STD_BEDTOOLS_INPUT_LABEL@ file" /> |
0 | 33 <!-- Additional files, if the user needs more --> |
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dde39ba9c031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
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34 <param argument="-bams" type="data" format="bam" multiple="true" label="BAM file" /> |
1 | 35 |
0 | 36 <expand macro="strand2" /> |
37 <expand macro="overlap" /> | |
1 | 38 <expand macro="reciprocal" /> |
0 | 39 <expand macro="split" /> |
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dde39ba9c031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents:
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40 <param argument="-q" type="integer" value="0" label="Minimum mapping quality (MAPQ) allowed" /> |
dde39ba9c031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
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41 <param name="duplicate" argument="-D" type="boolean" truevalue="-D" falsevalue="" checked="false" |
1 | 42 label="Include duplicate reads" |
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dde39ba9c031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
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43 help="Default counts non-duplicates only" /> |
dde39ba9c031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents:
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44 <param name="failed" argument="-F" type="boolean" truevalue="-F" falsevalue="" checked="false" |
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7308cc546a36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
iuc
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45 label="Include failed-QC reads" |
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dde39ba9c031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
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46 help="Default counts pass-QC reads only"/> |
dde39ba9c031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
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47 <param name="proper" argument="-p" type="boolean" truevalue="-p" falsevalue="" checked="false" |
1 | 48 label="Only count proper pairs" |
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dde39ba9c031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents:
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49 help="Default counts all alignments with MAPQ > -q argument, regardless of the BAM FLAG field" /> |
0 | 50 </inputs> |
51 <outputs> | |
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dde39ba9c031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
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52 <data name="output" format_source="input" metadata_source="input" /> |
0 | 53 </outputs> |
1 | 54 <tests> |
55 <test> | |
56 <param name="input" value="multiCov1.bed" ftype="bed" /> | |
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c78cf6fe3018
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 44bebb8a97d64015cbba59f0663e2541035112b6
iuc
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57 <param name="bams" value="srma_in3.bam,srma_in3.bam" ftype="bam"/> |
1 | 58 <param name="q" value="1"/> |
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dde39ba9c031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
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59 <param name="split" value=""/> |
1 | 60 <output name="output" file="multiCovBed_result1.bed" ftype="bed" /> |
61 </test> | |
62 </tests> | |
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dde39ba9c031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
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63 <help><![CDATA[ |
0 | 64 **What it does** |
65 | |
66 bedtools multicov, reports the count of alignments from multiple position-sorted and indexed BAM files that overlap intervals in a BED file. Specifically, for each BED interval provided, it reports a separate count of overlapping alignments from each BAM file. | |
67 | |
68 @REFERENCES@ | |
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dde39ba9c031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
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69 ]]></help> |
0 | 70 <expand macro="citations" /> |
71 </tool> |