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comparison sortmerna.xml @ 7:152bd01a4e76 draft

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planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit ac257f4227abec655c923fe377af182588b6d7bf-dirty
author bebatut
date Thu, 05 Nov 2015 09:09:06 -0500
parents 817fb14fc739
children 941ebfa59d1a
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6:817fb14fc739 7:152bd01a4e76
119 <param name="fastx_test" type='select' label="Output into Fasta/FastQ file?" help=""> 119 <param name="fastx_test" type='select' label="Output into Fasta/FastQ file?" help="">
120 <option value="--fastx">Yes</option> 120 <option value="--fastx">Yes</option>
121 <option value="">No</option> 121 <option value="">No</option>
122 </param> 122 </param>
123 <when value="--fastx"> 123 <when value="--fastx">
124 <param name='fastx_rejected' type='boolean' label="Conserve rejected reads?" help=""/> 124 <param name='fastx_rejected' type='boolean' checked="true" label="Conserve rejected reads?" help=""/>
125 </when> 125 </when>
126 </conditional> 126 </conditional>
127 127
128 <conditional name="sam"> 128 <conditional name="sam">
129 <param name="sam_test" type='select' label="Output SAM alignments?" help=""> 129 <param name="sam_test" type='select' label="Output SAM alignments?" help="">
234 <tests> 234 <tests>
235 <test> 235 <test>
236 <param name="input_sequence_file" value="input_sequences.fastq" ftype="fastq"/> 236 <param name="input_sequence_file" value="input_sequences.fastq" ftype="fastq"/>
237 <param name="databases_selector" value="history" /> 237 <param name="databases_selector" value="history" />
238 <param name="databases_name" value="db.fasta" ftype="fasta"/> 238 <param name="databases_name" value="db.fasta" ftype="fasta"/>
239 <param name="fastx_test" value="--fastx" />
240 <param name='fastx_rejected' value="True"/>
241 <param name="sam_test" value="" />
242 <param name="blast_format" value="--blast 3" />
243 <param name='log' value="" />
244 <param name="report_type" value="best" />
245 <param name="report_best_type" value="1" />
246 <param name="report_best_min_lis" value="2" />
247 <param name="e_value" value="1" />
248 <param name="match" value="2" />
249 <param name="mismatch" value="-3" />
250 <param name="gap_open" value="5" />
251 <param name="gap_ext" value="2" />
252 <param name="ambiguous_letter" value="-3" />
253 <param name="strand" value="both" />
254 <param name="seed_length" value="18" />
255 <param name="max_pos" value="10000" />
239 256
240 <output name="aligned_sequence_file" file="aligned_sequences.fastq" ftype="fastq"/> 257 <output name="aligned_sequence_file" file="aligned_sequences.fastq" ftype="fastq"/>
241 <output name="rejected_sequence_file" file="rejected_sequences.fastq" ftype="fastq"/> 258 <output name="rejected_sequence_file" file="rejected_sequences.fastq" ftype="fastq"/>
242 <output name="blast_output_file" file="blast_output.tabular" ftype="tabular"/> 259 <output name="blast_output_file" file="blast_output.tabular" ftype="tabular"/>
243 <output name="sam_alignment_file" file="sam_alignments.sam" ftype="sam"/>
244 </test> 260 </test>
245 </tests> 261 </tests>
246 262
247 <help><![CDATA[ 263 <help><![CDATA[
248 264