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comparison macros.xml @ 7:fcadce4d9a06 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
author bgruening
date Sat, 06 May 2017 13:18:09 -0400
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6:0f8646f22b8d 7:fcadce4d9a06
1 <?xml version='1.0' encoding='UTF-8'?>
2 <macros>
3 <token name="@WRAPPER_VERSION@">0.14</token>
4 <xml name="requirements_stdio">
5 <requirements>
6 <requirement type="package" version="0.1.19">samtools</requirement>
7 <yield/>
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 <version_command>bismark --version</version_command>
16 </xml>
17
18 <xml name="single_paired_conditional">
19 <!-- Input Parameters -->
20 <conditional name="singlePaired">
21 <param name="sPaired" type="select" label="Is this library mate-paired?">
22 <option value="single">Single-end</option>
23 <option value="paired">Paired-end</option>
24 </param>
25 <when value="single">
26 <param name="input_singles" type="data" format="fastqsanger,fastqillumina,fastq,fasta" label="FASTQ/FASTA file" help="FASTQ or FASTA files." />
27 </when>
28 <when value="paired">
29 <repeat name="mate_list" title="Paired End Pairs" min="1">
30 <param name="input_mate1" type="data" format="fastqsanger,fastqillumina,fastq,fasta" label="Mate pair 1" help="FASTQ or FASTA files." />
31 <param name="input_mate2" type="data" format="fastqsanger,fastqillumina,fastq,fasta" label="Mate pair 2" help="FASTQ or FASTA files." />
32 </repeat>
33 <param name="minInsert" type="integer" value="0" label="Minimum insert size for valid paired-end alignments" />
34 <param name="maxInsert" type="integer" value="500" label="Maximum insert size for valid paired-end alignments" />
35 </when>
36 </conditional>
37 </xml>
38
39 <xml name="advanced_params">
40 <param name="seed_len" type="integer" value="28" label="Seed length"
41 help="The number of bases of the high quality end of the read to which the maximum number of mismatches applies. (--seed-len)" />
42 <param name="qupto" type="integer" value="0" min="0" label="Only aligns the first N reads or read pairs from the input"
43 help="Default is 0 and means 'no-limit'. (--qupto)"/>
44 <param name="skip_reads" type="integer" value="0" label="Skip (i.e. do not align) the first N reads or read pairs from the input"
45 help="(--skip-reads)" />
46
47 <param name="suppressed_read_file" type="boolean" truevalue="true" falsevalue="false" checked="false"
48 label="Write ambiguous reads to an extra output file"
49 help="Write all reads which produce more than one valid alignment with the same number of lowest
50 mismatches or other reads that fail to align uniquely. (--output-suppressed-reads-r/l)" />
51 <param name="unmapped_read_file" type="boolean" truevalue="true" falsevalue="false" checked="false"
52 label="Write all reads that could not be aligned to a file. (--output-unmapped-reads-r/l)" />
53
54 <!-- output Options -->
55 <param name="bismark_stdout" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Write the bismark output and summary information to an extra file" />
56 <param name="isReportOutput" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Offer all report files concatenated in one file" />
57 <!--end output options -->
58
59 </xml>
60 <xml name="citation">
61 <citations>
62 <citation type="doi">10.1093/bioinformatics/btr167</citation>
63 </citations>
64 </xml>
65 </macros>