Mercurial > repos > iuc > bedtools
comparison multiCov.xml @ 34:dde39ba9c031 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
author | iuc |
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date | Mon, 29 Apr 2019 05:55:48 -0400 |
parents | 4f7a5ccd2ae9 |
children | 3e38c9b3214f |
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33:87ee588b3d45 | 34:dde39ba9c031 |
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1 <tool id="bedtools_multicovtbed" name="bedtools MultiCovBed" version="@WRAPPER_VERSION@"> | 1 <tool id="bedtools_multicovtbed" name="bedtools MultiCovBed" version="@TOOL_VERSION@"> |
2 <description>counts coverage from multiple BAMs at specific intervals</description> | 2 <description>counts coverage from multiple BAMs at specific intervals</description> |
3 <macros> | 3 <macros> |
4 <import>macros.xml</import> | 4 <import>macros.xml</import> |
5 </macros> | 5 </macros> |
6 <expand macro="requirements" /> | 6 <expand macro="requirements" /> |
7 <expand macro="stdio" /> | 7 <expand macro="stdio" /> |
8 <command> | 8 <command><![CDATA[ |
9 <![CDATA[ | 9 #for $i, $bam in enumerate($bams): |
10 #for $i, $bam in enumerate( $bams ): | 10 ln -s -f '$bam' ${i}.bam && |
11 ln -s -f $bam ${i}.bam && | 11 ln -s -f '$bam.metadata.bam_index' ${i}.bam.bai && |
12 ln -s -f $bam.metadata.bam_index ${i}.bam.bai && | 12 #end for |
13 #end for | |
14 | 13 |
15 bedtools multicov | 14 bedtools multicov |
16 -bed '$input' | 15 -bed '$input' |
17 -bams | 16 -bams |
18 #for $i, $bam in enumerate( $bams ): | 17 #for $i, $bam in enumerate($bams): |
19 '${i}.bam' | 18 '${i}.bam' |
20 #end for | 19 #end for |
21 $strand | 20 $strand |
22 -f $overlap | 21 @OVERLAP@ |
23 $reciprocal | 22 $reciprocal |
24 $split | 23 $split |
25 -q $q | 24 -q $q |
26 $duplicate | 25 $duplicate |
27 $failed | 26 $failed |
28 $proper | 27 $proper |
29 > '$output' | 28 > '$output' |
30 ]]> | 29 ]]></command> |
31 </command> | |
32 <inputs> | 30 <inputs> |
33 <param name="input" format="@STD_BEDTOOLS_INPUTS@" type="data" label="Sorted @STD_BEDTOOLS_INPUT_LABEL@ file" /> | 31 <param name="input" argument="-bed" type="data" format="@STD_BEDTOOLS_INPUTS@" label="Sorted @STD_BEDTOOLS_INPUT_LABEL@ file" /> |
34 <!-- Additional files, if the user needs more --> | 32 <!-- Additional files, if the user needs more --> |
35 <param name="bams" format="bam" type="data" multiple="True" label="BAM file" /> | 33 <param argument="-bams" type="data" format="bam" multiple="true" label="BAM file" /> |
36 | 34 |
37 <expand macro="strand2" /> | 35 <expand macro="strand2" /> |
38 <expand macro="overlap" /> | 36 <expand macro="overlap" /> |
39 <expand macro="reciprocal" /> | 37 <expand macro="reciprocal" /> |
40 <expand macro="split" /> | 38 <expand macro="split" /> |
41 <param name="q" type="integer" value="0" label="Minimum mapping quality (MAPQ) allowed" help="(-q)" /> | 39 <param argument="-q" type="integer" value="0" label="Minimum mapping quality (MAPQ) allowed" /> |
42 <param name="duplicate" type="boolean" checked="False" truevalue="-D" falsevalue="" | 40 <param name="duplicate" argument="-D" type="boolean" truevalue="-D" falsevalue="" checked="false" |
43 label="Include duplicate reads" | 41 label="Include duplicate reads" |
44 help="Default counts non-duplicates only. (-D)" /> | 42 help="Default counts non-duplicates only" /> |
45 <param name="failed" type="boolean" checked="false" truevalue="-F" falsevalue="" | 43 <param name="failed" argument="-F" type="boolean" truevalue="-F" falsevalue="" checked="false" |
46 label="Include failed-QC reads" | 44 label="Include failed-QC reads" |
47 help="Default counts pass-QC reads only (-F)"/> | 45 help="Default counts pass-QC reads only"/> |
48 <param name="proper" type="boolean" checked="false" truevalue="-p" falsevalue="" | 46 <param name="proper" argument="-p" type="boolean" truevalue="-p" falsevalue="" checked="false" |
49 label="Only count proper pairs" | 47 label="Only count proper pairs" |
50 help="Default counts all alignments with MAPQ > -q argument, regardless of the BAM FLAG field. (-p)" /> | 48 help="Default counts all alignments with MAPQ > -q argument, regardless of the BAM FLAG field" /> |
51 </inputs> | 49 </inputs> |
52 <outputs> | 50 <outputs> |
53 <data name="output" metadata_source="input" format_source="input" /> | 51 <data name="output" format_source="input" metadata_source="input" /> |
54 </outputs> | 52 </outputs> |
55 <tests> | 53 <tests> |
56 <test> | 54 <test> |
57 <param name="input" value="multiCov1.bed" ftype="bed" /> | 55 <param name="input" value="multiCov1.bed" ftype="bed" /> |
58 <param name="bams" value="srma_in3.bam,srma_in3.bam" ftype="bam"/> | 56 <param name="bams" value="srma_in3.bam,srma_in3.bam" ftype="bam"/> |
59 <param name="q" value="1"/> | 57 <param name="q" value="1"/> |
60 <param name="split" value="False"/> | 58 <param name="split" value=""/> |
61 <output name="output" file="multiCovBed_result1.bed" ftype="bed" /> | 59 <output name="output" file="multiCovBed_result1.bed" ftype="bed" /> |
62 </test> | 60 </test> |
63 </tests> | 61 </tests> |
64 <help> | 62 <help><![CDATA[ |
65 <![CDATA[ | |
66 **What it does** | 63 **What it does** |
67 | 64 |
68 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. | 65 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. |
69 | 66 |
70 | |
71 @REFERENCES@ | 67 @REFERENCES@ |
72 ]]> | 68 ]]></help> |
73 </help> | |
74 <expand macro="citations" /> | 69 <expand macro="citations" /> |
75 </tool> | 70 </tool> |