Mercurial > repos > peterjc > mira4_assembler

comparison tools/mira4_0/mira4_mapping.xml @ 33:1291ed21789f draft

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planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 1d7d466d01b23d03d214e93f1f8efa19cfa18268
author peterjc
date Fri, 02 Jun 2017 11:22:01 -0400
parents 56b421d59805
children 259891fce7fd
comparison
equal deleted inserted replaced
32:56b421d59805 33:1291ed21789f
154 <when value="none" /><!-- no further questions --> 154 <when value="none" /><!-- no further questions -->
155 </conditional> 155 </conditional>
156 <param name="filenames" type="data" format="fastq,mira" multiple="true" optional="false" label="Read file(s)" 156 <param name="filenames" type="data" format="fastq,mira" multiple="true" optional="false" label="Read file(s)"
157 help="Multiple files allowed, for example paired reads can be given as two files (MIRA looks at read names to identify pairs)." /> 157 help="Multiple files allowed, for example paired reads can be given as two files (MIRA looks at read names to identify pairs)." />
158 </repeat> 158 </repeat>
159 <param name="maf_wanted" type="boolean" label="Output mapping in MIRA's own format?" checked="False" /> 159 <param name="maf_wanted" type="boolean" label="Output mapping in MIRA's own format?" checked="false" />
160 <param name="bam_wanted" type="boolean" label="Convert mapping into BAM format?" checked="True" /> 160 <param name="bam_wanted" type="boolean" label="Convert mapping into BAM format?" checked="true" />
161 </inputs> 161 </inputs>
162 <outputs> 162 <outputs>
163 <data name="out_fasta" format="fasta" label="MIRA #if str($strain_setup)=='same' then 'same strain' else 'reference' # mapping contigs (FASTA)" /> 163 <data name="out_fasta" format="fasta" label="MIRA #if str($strain_setup)=='same' then 'same strain' else 'reference' # mapping contigs (FASTA)" />
164 <data name="out_bam" format="bam" label="MIRA #if str($strain_setup)=='same' then 'same strain' else 'reference' # mapping assembly (BAM)"> 164 <data name="out_bam" format="bam" label="MIRA #if str($strain_setup)=='same' then 'same strain' else 'reference' # mapping assembly (BAM)">
165 <filter>bam_wanted is True</filter> 165 <filter>bam_wanted is True</filter>