Mercurial > repos > bgruening > suspenders
comparison suspenders.xml @ 0:35b4ff47bf09 draft
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author | bgruening |
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date | Sat, 02 Aug 2014 11:18:24 -0400 |
parents | |
children | 7a5fa8282f82 |
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-1:000000000000 | 0:35b4ff47bf09 |
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1 <?xml version="1.0"?> | |
2 <tool name="suspenders" id="bg_suspenders" version="0.2.5.0"> | |
3 <description>merging of labeled alignments</description> | |
4 <requirements> | |
5 <requirement type="package" version="0.2.5">suspenders</requirement> | |
6 <requirement type="package" version="1.2.1">matplotlib</requirement> | |
7 <requirement type="package" version="0.7.7">pysam</requirement> | |
8 </requirements> | |
9 <stdio> | |
10 <exit_code range="1:" /> | |
11 <exit_code range=":-1" /> | |
12 <regex match="Error:" /> | |
13 <regex match="Exception:" /> | |
14 </stdio> | |
15 <command> | |
16 <![CDATA[ | |
17 #set $inputs = "" | |
18 #for $counter, $input_bam in enumerate( $reference_source.input_bams ): | |
19 ln -s "${input_bam.input_bam}" "${counter}.bam"; | |
20 ln -s "${input_bam.input_bam.metadata.bam_index}" "${counter}.bai"; | |
21 set $inputs += '%s ' % $counter | |
22 #end for | |
23 | |
24 pysuspenders | |
25 $labels | |
26 $union | |
27 $quality | |
28 $pileup | |
29 $image | |
30 $mate_all | |
31 $union_all | |
32 $random_filter | |
33 #if $chart: | |
34 -c $image | |
35 #end if | |
36 -p \${GALAXY_SLOTS:-4} | |
37 $output | |
38 $inputs | |
39 ]]> | |
40 </command> | |
41 <inputs> | |
42 <repeat name="input_bams" title="BAM files" min="2" help="sorted by read name"> | |
43 <param name="input_bam" type="data" format="bam" label="BAM file"> | |
44 <validator type="unspecified_build" /> | |
45 <validator type="dataset_metadata_in_data_table" table_name="gatk2_picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /> <!-- fixme!!! this needs to be a select --> | |
46 </param> | |
47 </repeat> | |
48 | |
49 <param name="labels" type="boolean" truevalue="--lapels" falsevalue="--normal-input" | |
50 checked="True" | |
51 label="Input has lapels tags" help="--lapels/--normal-input" /> | |
52 | |
53 <param name="union" type="boolean" truevalue="--union" falsevalue="" | |
54 label="Merge the files using the union filter" help="--union"/> | |
55 | |
56 <param name="quality" type="boolean" truevalue="--quality" falsevalue="" | |
57 checked="True" label="Merge the files using the quality filter" help="--quality"/> | |
58 | |
59 <param name="pileup" type="boolean" truevalue="--pileup" falsevalue="" | |
60 label="merge the files using the quality filter, then the pileup height filter" help="--pileup"/> | |
61 | |
62 <param name="chart" type="boolean" truevalue="True" falsevalue="False" | |
63 label="save pileup chart to an image" help=""/> | |
64 | |
65 <param name="mate_all" type="boolean" truevalue="--mate-all" falsevalue="" | |
66 label="compare unmated segments to mated ones" help="--mate-all"/> | |
67 | |
68 <param name="union_all" type="boolean" truevalue="--union-all" falsevalue="" | |
69 label="Use union filter if other filters fail" help="always active for --union (--union-all)"/> | |
70 | |
71 <param name="random_filter" type="boolean" truevalue="--random-filer" falsevalue="" | |
72 label="Use random filter if other filters fail" help="default for --quality and --pileup (--random-filter)"/> | |
73 | |
74 </inputs> | |
75 <outputs> | |
76 <data name="output" format="bam" label="${tool.name} on ${on_string}"/> | |
77 <data name="image" format="png" label="${tool.name} on ${on_string}: Chart"> | |
78 <filter>chart is True</filter> | |
79 <data> | |
80 </outputs> | |
81 <tests> | |
82 | |
83 </tests> | |
84 <help> | |
85 <![CDATA[ | |
86 | |
87 **What it does** | |
88 | |
89 Allows the merging of alignments that have been annotated using pylapels into a single alignment that picks the highest quality alignment. | |
90 | |
91 https://pypi.python.org/pypi/suspenders/ | |
92 | |
93 ]]> | |
94 </help> | |
95 </tool> |