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comparison sortmerna.xml @ 3:59252ca85c74 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 5a8ffc52b7076d8d4fbc9649703bb4c0155b726c
author rnateam
date Wed, 15 Jun 2016 05:31:46 -0400
parents 3699b6b771e0
children 1bdb57965c6f
comparison
equal deleted inserted replaced
2:3699b6b771e0 3:59252ca85c74
1 <tool id="bg_sortmerna" name="Filter with SortMeRNA" version="2.1b.0"> 1 <tool id="bg_sortmerna" name="Filter with SortMeRNA" version="2.1b.1">
2 <description>Fast and accurate filtering of ribosomal RNAs in metatranscriptomic data</description> 2 <description>Fast and accurate filtering of ribosomal RNAs in metatranscriptomic data</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="2.1b">sortmerna</requirement> 4 <requirement type="package" version="2.1b">sortmerna</requirement>
5 </requirements> 5 </requirements>
6 <stdio> 6 <stdio>
73 #end if 73 #end if
74 $aligned_sam.aligned_sam_selector 74 $aligned_sam.aligned_sam_selector
75 #if $aligned_sam.aligned_sam_selector == '--sam' 75 #if $aligned_sam.aligned_sam_selector == '--sam'
76 $aligned_sam.sq 76 $aligned_sam.sq
77 #end if 77 #end if
78 $aligned_blast 78 #if $aligned_blast.aligned_blast_selector == '--blast'
79 --blast "$aligned_blast.aligned_blast_format"
80 #end if
79 81
80 $log 82 $log
81 83
82 #if $report.report_type == 'best' 84 #if $report.report_type == 'best'
83 #if $report.report_best.report_best_type == '1' 85 #if $report.report_best.report_best_type == '1'
177 <when value="--sam"> 179 <when value="--sam">
178 <param name="sq" type="boolean" truevalue="--SQ" falsevalue="" label="Add SQ tags to the SAM file" help="(--SQ)" /> 180 <param name="sq" type="boolean" truevalue="--SQ" falsevalue="" label="Add SQ tags to the SAM file" help="(--SQ)" />
179 </when> 181 </when>
180 <when value="" /> 182 <when value="" />
181 </conditional> 183 </conditional>
182 <param name="aligned_blast" type="select" label="Include alignments in BLAST-like format"> 184 <conditional name="aligned_blast">
183 <option value="--blast 0">pairwise (--blast 0)</option> 185 <param name="aligned_blast_selector" type="select" label="Include alignments in BLAST-like format?">
184 <option value="--blast 1">tabular BLAST -m 8 format (--blast 1)</option> 186 <option value="--blast">Yes</option>
185 <option value="--blast 2">tabular + column for CIGAR (--blast 2)</option> 187 <option value="" selected="true">No</option>
186 <option value="--blast 3">tabular + columns for CIGAR and query coverage (--blast 3)</option> 188 </param>
187 <option value="" selected="true">No</option> 189 <when value="--blast">
188 </param> 190 <param name="aligned_blast_format" type="select" label="BLAST-like format?">
189 <param name="log" type="boolean" checked="False" truevalue="--log" falsevalue="" label="Generate statistics file" 191 <option value="0">pairwise (--blast '0')</option>
192 <option value="1">tabular BLAST -m 8 format (--blast '1')</option>
193 <option value="1 cigar">tabular + column for CIGAR (--blast '1 cigar')</option>
194 <option value="1 cigar qcov">tabular + columns for CIGAR and query coverage (--blast '1 cigar qcov')</option>
195 <option value="1 cigar qcov qstrand">tabular + columns for CIGAR, query coverage and strand (--blast '1 cigar qcov qstrand')</option>
196 </param>
197 </when>
198 <when value="" />
199 </conditional>
200 <param name="log" type="boolean" checked="false" truevalue="--log" falsevalue="" label="Generate statistics file"
190 help="Generates statistics for the rRNA content of reads, as well as rRNA subunit distribution. (--log)"> 201 help="Generates statistics for the rRNA content of reads, as well as rRNA subunit distribution. (--log)">
191 </param> 202 </param>
192 <conditional name="report"> 203 <conditional name="report">
193 <param name="report_type" type="select" label="Parameters for filtering and read mapping" help=""> 204 <param name="report_type" type="select" label="Parameters for filtering and read mapping" help="">
194 <option value="best" selected="true">Report best alignments per read reaching E-value</option> 205 <option value="best" selected="true">Report best alignments per read reaching E-value</option>
245 label="Alignments on ${on_string} (SAM)"> 256 label="Alignments on ${on_string} (SAM)">
246 <filter>aligned_sam['aligned_sam_selector']</filter> 257 <filter>aligned_sam['aligned_sam_selector']</filter>
247 </data> 258 </data>
248 <data format="tabular" name="output_blast" from_work_dir="aligned.blast" 259 <data format="tabular" name="output_blast" from_work_dir="aligned.blast"
249 label="Alignments on ${on_string} (BLAST)"> 260 label="Alignments on ${on_string} (BLAST)">
250 <filter>aligned_blast</filter> 261 <filter>aligned_blast['aligned_blast_selector']</filter>
251 <change_format> 262 <change_format>
252 <when input="aligned_blast" value="--blast 0" format="txt" /> 263 <when input="aligned_blast.aligned_blast_format" value="0" format="txt" />
253 </change_format> 264 </change_format>
254 </data> 265 </data>
255 <data format="txt" name="output_log" label="${tool.name} statistics (txt)" from_work_dir="aligned.log"> 266 <data format="txt" name="output_log" label="${tool.name} statistics (txt)" from_work_dir="aligned.log">
256 <filter>log</filter> 267 <filter>log</filter>
257 </data> 268 </data>
261 <param name="input_reads" value="read_small.fastq" /> 272 <param name="input_reads" value="read_small.fastq" />
262 <param name="sequencing_type_selector" value="not_paired" /> 273 <param name="sequencing_type_selector" value="not_paired" />
263 <param name="strand_search" value="" /> 274 <param name="strand_search" value="" />
264 <param name="databases_selector" value="history" /> 275 <param name="databases_selector" value="history" />
265 <param name="database_name" value="ref_small.fasta" /> 276 <param name="database_name" value="ref_small.fasta" />
277 <param name="aligned_fastx_selector" value="--fastx" />
266 <param name="other" value="True" /> 278 <param name="other" value="True" />
279 <param name="aligned_sam_selector" value="--sam" />
280 <param name="aligned_blast_selector" value="--blast"/>
281 <param name="aligned_blast_format" value="1 cigar qcov" />
267 <param name="log" value="" /> 282 <param name="log" value="" />
283 <param name="report_type" value="best" />
284 <param name="report_best_type" value="1" />
285 <param name="e_value" value="1"/>
286 <param name="match" value="2"/>
287 <param name="mismatch" value="-3" />
288 <param name="gap_open" value="5"/>
289 <param name="gap_ext" value="2"/>
290 <param name="ambiguous_letter" value="-3"/>
268 <output name="output_fastx" file="sortmerna_wrapper_accept1.fastq" /> 291 <output name="output_fastx" file="sortmerna_wrapper_accept1.fastq" />
269 <output name="output_other" file="sortmerna_wrapper_other1.fastq" /> 292 <output name="output_other" file="sortmerna_wrapper_other1.fastq" />
270 <output name="output_sam" file="sortmerna_wrapper_sam1.sam" lines_diff="2" /> 293 <output name="output_sam" file="sortmerna_wrapper_sam1.sam" lines_diff="2" />
271 </test> 294 </test>
272 <test> 295 <test>
273 <param name="input_reads" value="read_small.fasta" /> 296 <param name="input_reads" value="read_small.fasta" />
274 <param name="sequencing_type_selector" value="not_paired" /> 297 <param name="sequencing_type_selector" value="not_paired" />
275 <param name="strand_search" value="" /> 298 <param name="strand_search" value="" />
276 <param name="databases_selector" value="history" /> 299 <param name="databases_selector" value="history" />
277 <param name="database_name" value="ref_small.fasta" /> 300 <param name="database_name" value="ref_small.fasta" />
301 <param name="aligned_fastx_selector" value="--fastx" />
278 <param name="other" value="True" /> 302 <param name="other" value="True" />
303 <param name="aligned_sam_selector" value="--sam" />
304 <param name="aligned_blast" value="" />
279 <param name="log" value="" /> 305 <param name="log" value="" />
306 <param name="report_type" value="best" />
307 <param name="report_best_type" value="1" />
308 <param name="report_type" value="best" />
309 <param name="report_best_type" value="1" />
310 <param name="e_value" value="1"/>
311 <param name="match" value="2"/>
312 <param name="mismatch" value="-3" />
313 <param name="gap_open" value="5"/>
314 <param name="gap_ext" value="2"/>
315 <param name="ambiguous_letter" value="-3"/>
280 <output name="output_fastx" file="sortmerna_wrapper_accept2.fasta" /> 316 <output name="output_fastx" file="sortmerna_wrapper_accept2.fasta" />
281 <output name="output_other" file="sortmerna_wrapper_other2.fasta" /> 317 <output name="output_other" file="sortmerna_wrapper_other2.fasta" />
282 <output name="output_sam" file="sortmerna_wrapper_sam2.sam" lines_diff="2" /> 318 <output name="output_sam" file="sortmerna_wrapper_sam2.sam" lines_diff="2" />
283 </test> 319 </test>
284 </tests> 320 </tests>