Mercurial > repos > bebatut > sortmerna

comparison sortmerna.xml @ 3:9c19086ae626 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 4d9df680f128bc18183ebba6f85fc24f11207571-dirty
author bebatut
date Wed, 28 Oct 2015 08:23:45 -0400
parents 48ab7cdab700
children 5d7ec21f6d4c
comparison
equal deleted inserted replaced
2:48ab7cdab700 3:9c19086ae626
39 && 39 &&
40 40
41 sortmerna 41 sortmerna
42 --ref $ref 42 --ref $ref
43 --reads $input_sequence_file 43 --reads $input_sequence_file
44 --aligned aligned
44 45
45 #if $fastx.test: 46 #if $fastx.test:
46 --aligned $aligned_sequence_file
47 --fastx 47 --fastx
48 #if $fastx.rejected: 48 #if $fastx.rejected:
49 --other $rejected_sequence_file 49 --other other_file
50 #end if 50 #end if
51 #end if 51 #end if
52 52
53 #if $sam.test: 53 #if $sam.test:
54 --aligned $sam_alignment_file 54 --aligned $sam_alignment_file
56 $sam.sq_tag 56 $sam.sq_tag
57 #end if 57 #end if
58 58
59 #if $blast.test: 59 #if $blast.test:
60 --aligned $blast_output_file 60 --aligned $blast_output_file
61 --blast '$blast.format' 61 --blast "$blast.format"
62 #end if 62 #end if
63
64 $log.test
63 65
64 #if $report.type == 'best': 66 #if $report.type == 'best':
65 #if $report.best.type == '0': 67 #if $report.best.type == '0':
66 --best 0 68 --best 0
67 #else if $report.best.type == '1': 69 #else if $report.best.type == '1':
140 <option value="1 cigar">Tabular + column for CIGAR</option> 142 <option value="1 cigar">Tabular + column for CIGAR</option>
141 <option value="1 cigar qcov" selected="true">Tabular + columns for CIGAR and query coverage</option> 143 <option value="1 cigar qcov" selected="true">Tabular + columns for CIGAR and query coverage</option>
142 <option value="1 cigar qcov qstrand">Tabular + columns for CIGAR, query coverage and strand</option> 144 <option value="1 cigar qcov qstrand">Tabular + columns for CIGAR, query coverage and strand</option>
143 </param> 145 </param>
144 </when> 146 </when>
147 </conditional>
148
149 <conditional name="log">
150 <param name='test' type='boolean' checked="true" truevalue='--log' falsevalue='' label="Conserve overall statistic output into a log file?" help=""/>
145 </conditional> 151 </conditional>
146 152
147 <conditional name="report"> 153 <conditional name="report">
148 <param name="type" type="select" display="radio" label="Parameters for filtering and read mapping" help=""> 154 <param name="type" type="select" display="radio" label="Parameters for filtering and read mapping" help="">
149 <option value="best" selected="true">Report best alignments per read reaching E-value</option> 155 <option value="best" selected="true">Report best alignments per read reaching E-value</option>
195 <param name="seed_length" type="integer" min="0" max="100" value="18" label="Seed length for database indexing" help=""/> 201 <param name="seed_length" type="integer" min="0" max="100" value="18" label="Seed length for database indexing" help=""/>
196 <param name="max_pos" type="integer" min="0" max="100000" value="10000" label="Maximum number of positions to store for each k-mer for database indexing" help="With 0, all positions are stored"/> 202 <param name="max_pos" type="integer" min="0" max="100000" value="10000" label="Maximum number of positions to store for each k-mer for database indexing" help="With 0, all positions are stored"/>
197 </inputs> 203 </inputs>
198 204
199 <outputs> 205 <outputs>
200 <data format="fastq,fasta" name="aligned_sequence_file" metadata="input_sequence_file"> 206 <data format_source="input_sequence_file" name="aligned_sequence_file" metadata="input_sequence_file" from_work_dir="aligned.dat">
201 <filter>((fastx['test']))</filter> 207 <filter>((fastx['test']))</filter>
202 </data> 208 </data>
203 209
204 <data format="fastq,fasta" name="rejected_sequence_file" metadata="input_sequence_file"> 210 <data format_source="input_sequence_file" name="rejected_sequence_file" metadata="input_sequence_file" from_work_dir="other_file.dat">
205 <filter>((fastx['test'] and fastx['rejected']))</filter> 211 <filter>((fastx['test'] and fastx['rejected']))</filter>
206 </data> 212 </data>
207 213
208 <data format="sam" name="sam_alignment_file" metadata="input_sequence_file"> 214 <data format="sam" name="sam_alignment_file" metadata="input_sequence_file" from_work_dir="aligned.sam">
209 <filter>((sam['test']]))</filter> 215 <filter>((sam['test']]))</filter>
210 </data> 216 </data>
211 217
212 <data format="text" name="blast_output_file" metadata="input_sequence_file"> 218 <data format="tabular" name="blast_output_file" metadata="input_sequence_file" from_work_dir="aligned.blast">
213 <filter>((blast['test']))</filter> 219 <filter>((blast['test']))</filter>
220 <change_format>
221 <when input="blast.format" value="0" format="txt" />
222 </change_format>
223 </data>
224
225 <data format="txt" name="output_log" metadata="input_sequence_file" from_work_dir="aligned.log">
226 <filter>log.test</filter>
214 </data> 227 </data>
215 </outputs> 228 </outputs>
216 229
217 <tests> 230 <tests>
218 <test> 231 <test>