Mercurial > repos > iuc > bbtools_bbmap

comparison bbmap.xml @ 2:e0ca2ec4f5d9 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
author iuc
date Thu, 11 Nov 2021 16:38:09 +0000
parents 07a6e49c7d74
children 8157a81f511c
comparison
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1:17ad142b56e6 2:e0ca2ec4f5d9
59 #else: 59 #else:
60 out='mapped.bam' && mv 'mapped.bam' '$output' 60 out='mapped.bam' && mv 'mapped.bam' '$output'
61 #end if 61 #end if
62 ]]></command> 62 ]]></command>
63 <inputs> 63 <inputs>
64 <conditional name="input_type_cond"> 64 <expand macro="input_type_cond"/>
65 <param name="input_type" type="select" label="Choose the category of the files to be analyzed">
66 <option value="single" selected="true">Single dataset</option>
67 <option value="pair">Dataset pair</option>
68 <option value="paired">List of dataset pairs</option>
69 </param>
70 <when value="single">
71 <param name="read1" type="data" format="fastqsanger.gz,fastqsanger" label="Read1 fastq file"/>
72 </when>
73 <when value="pair">
74 <param name="read1" type="data" format="fastqsanger.gz,fastqsanger" label="Read1 fastq file"/>
75 <param name="read2" type="data" format="fastqsanger.gz,fastqsanger" label="Read2 fastq file"/>
76 </when>
77 <when value="paired">
78 <param name="reads_collection" type="data_collection" format="fastqsanger,fastqsanger.gz" collection_type="paired" label="Collection of fastqsanger paired read files"/>
79 </when>
80 </conditional>
81 <expand macro="reference_source_cond"/> 65 <expand macro="reference_source_cond"/>
82 <param name="output_sort" type="select" label="BAM sorting mode" help="The 'Not sorted' option can significantly extend the run time of the tool (it runs using a single thread)."> 66 <param name="output_sort" type="select" label="BAM sorting mode" help="The 'Not sorted' option can significantly extend the run time of the tool (it runs using a single thread).">
83 <option value="coordinate" selected="True">Sort by chromosomal coordinates</option> 67 <option value="coordinate" selected="True">Sort by chromosomal coordinates</option>
84 <option value="name">Sort by read names</option> 68 <option value="name">Sort by read names</option>
85 <option value="unsorted">Not sorted (sorted as input)</option> 69 <option value="unsorted">Not sorted (sorted as input)</option>