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comparison yaha.xml @ 3:bcba667aef5b draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 287ffa5c3b1d4f08c7633bddd9dd98925a5483c4-dirty
author mvdbeek
date Wed, 04 Jan 2017 05:04:09 -0500
parents 37cac55c1081
children e61ba2a4b8d9
comparison
equal deleted inserted replaced
2:37cac55c1081 3:bcba667aef5b
23 #else: 23 #else:
24 #pass ## augment with pre-built index if considered useful 24 #pass ## augment with pre-built index if considered useful
25 #end if 25 #end if
26 yaha 26 yaha
27 -x '$index_path' 27 -x '$index_path'
28 -q '$q' 28 #if str($readtype.single_or_paired) == "se":
29 -q '$reatype.input_single'
30 #else:
31 -q <(cat '$readtype.input_paired.forward' '$readtype.input_paired.reverse')
32 #end if
29 $outformat stdout 33 $outformat stdout
30 -t \${GALAXY_SLOTS:-1} 34 -t \${GALAXY_SLOTS:-1}
31 -BW $BW 35 -BW $BW
32 -G $G 36 -G $G
33 -H $H 37 -H $H
60 -FBS N 64 -FBS N
61 #end if 65 #end if
62 | sambamba view -S -f bam /dev/stdin | sambamba sort -o '$alignment' -l 6 -t \${GALAXY_SLOTS:-1} /dev/stdin 66 | sambamba view -S -f bam /dev/stdin | sambamba sort -o '$alignment' -l 6 -t \${GALAXY_SLOTS:-1} /dev/stdin
63 ]]></command> 67 ]]></command>
64 <inputs> 68 <inputs>
65 <param type="data" argument="q" label="Fastq reads to align" format="fastqsanger" /> 69 <conditional name="readtype">
70 <param name="single_or_paired" type="select" label="Single-end or paired-end reads?" help="Note: yaha does not take mate-pair information into account. If you select pe_collection, forward and reverse reads will be merged.">
71 <option value="se" selected="true">Single-end</option>
72 <option value="pe_collection">Paired-end (as collection)</option>
73 </param>
74 <when value="se">
75 <param format="fastqsanger,fastqsanger.gz" name="input_single" type="data" label="Single-end FASTQ reads" help="(-q)" />
76 </when>
77 <when value="pe_collection">
78 <param format="fastqsanger,fastqsanger.gz" name="input_paired" type="data_collection" collection_type="paired" label="Paired-end FASTQ reads as paired collection" help="(-q)"/>
79 </when>
80 </conditional>
66 <conditional name="reference_genome"> 81 <conditional name="reference_genome">
67 <param help="Built-in references were created using default options" label="Source for the reference genome to align against" name="reference_genome_source" type="select"> 82 <param help="Built-in references were created using default options" label="Source for the reference genome to align against" name="reference_genome_source" type="select">
68 <!-- Write a datamanager if prebuilt genomes are important 83 <!-- Write a datamanager if prebuilt genomes are important
69 <option selected="True" value="indexed">Use a built-in index</option> 84 <option selected="True" value="indexed">Use a built-in index</option>
70 --> 85 -->
71 <option value="history">Use a genome from history to build an index</option> 86 <option value="history">Use a genome from history to build an index</option>
72 <option value="reference">Use a built-in genome to build an index</option> 87 <option value="reference">Use a built-in genome to build an index</option>
73 </param> 88 </param>
89 <!--
74 <when value="indexed"> 90 <when value="indexed">
75 <param help="If your genome of interest is not listed, contact the Galaxy team" label="Select a reference genome" name="index" type="select"> 91 <param help="If your genome of interest is not listed, contact the Galaxy team" label="Select a reference genome" name="index" type="select">
76 <options from_data_table="yaha_indexes"> 92 <options from_data_table="yaha_indexes">
77 <filter column="2" type="sort_by" /> 93 <filter column="2" type="sort_by" />
78 <validator message="No genomes are available for the selected input dataset" type="no_options" /> 94 <validator message="No genomes are available for the selected input dataset" type="no_options" />
79 </options> 95 </options>
80 </param> 96 </param>
81 </when> 97 </when>
98 -->
82 <when value="history"> 99 <when value="history">
83 <param format="fasta" label="Select the reference genome" name="history_item" type="data" /> 100 <param format="fasta" label="Select the reference genome" name="history_item" type="data" />
84 <expand macro="index_parameter"/> 101 <expand macro="index_parameter"/>
85 </when> 102 </when>
86 <when value="reference"> 103 <when value="reference">