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comparison sortmerna.xml @ 16:1a4662c2d6db draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 044a991b45c9135339daf138929887cd8e93a1bf-dirty
author bebatut
date Mon, 12 Jun 2017 06:20:50 -0400
parents baab049d3aff
children 715c75d6d784
comparison
equal deleted inserted replaced
15:baab049d3aff 16:1a4662c2d6db
1 <tool id="bg_sortmerna" name="Filter with SortMeRNA" version="2.1.0"> 1 <tool id="bg_sortmerna" name="Filter with SortMeRNA" version="@VERSION@.4">
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 <macros>
4 <import>macros.xml</import>
5 </macros>
3 <requirements> 6 <requirements>
4 <requirement type="package" version="2.0">sortmerna</requirement> 7 <requirement type="package" version="@VERSION@">sortmerna</requirement>
5 </requirements> 8 </requirements>
6 <stdio> 9 <stdio>
7 <regex match="This program builds a Burst trie on an input rRNA database" 10 <regex match="This program builds a Burst trie on an input rRNA database"
8 source="both" 11 source="both"
9 level="fatal" 12 level="fatal"
33 #end for 36 #end for
34 #else if str( $databases_type.databases_selector ) == 'cached_to_index' 37 #else if str( $databases_type.databases_selector ) == 'cached_to_index'
35 ## databases path is not directly accessible, must match by hand with LOC file contents 38 ## databases path is not directly accessible, must match by hand with LOC file contents
36 #set $data_table = dict([(_[0], _[2]) for _ in $databases_type.input_databases.input.options.tool_data_table.data]) 39 #set $data_table = dict([(_[0], _[2]) for _ in $databases_type.input_databases.input.options.tool_data_table.data])
37 #for $db in $databases_type.input_databases.value 40 #for $db in $databases_type.input_databases.value
38 #set $ref += $sep + $data_table[$db] + ',' + $os.path.splitext($data_table[$db])[0] + '-reindexed' 41 #set $ref += $sep + $databases_type.input_databases.path + '.fasta,' + $databases_type.input_databases.path + '-reindexed'
39 #set $sep = ':' 42 #set $sep = ':'
40 #end for 43 #end for
41 #else: 44 #else:
42 ## databases path is not directly accessible, must match by hand with LOC file contents 45 ## databases path is not directly accessible, must match by hand with LOC file contents
43 #set $data_table = dict([(_[0], _[2]) for _ in $databases_type.input_databases.input.options.tool_data_table.data]) 46 #set $data_table = dict([(_[0], _[2]) for _ in $databases_type.input_databases.input.options.tool_data_table.data])
44 #for $db in $databases_type.input_databases.value 47 #for $db in $databases_type.input_databases.value
45 #set $ref += $sep + $data_table[$db] + ',' + $os.path.splitext($data_table[$db])[0] 48 #set $ref += $sep + $databases_type.input_databases.path + '.fasta,' + $databases_type.input_databases.path
46 #set $sep = ':' 49 #set $sep = ':'
47 #end for 50 #end for
48 #end if 51 #end if
49 52
50 #if str( $databases_type.databases_selector ) != 'cached': 53 #if str( $databases_type.databases_selector ) != 'cached':
73 #end if 76 #end if
74 $aligned_sam.aligned_sam_selector 77 $aligned_sam.aligned_sam_selector
75 #if $aligned_sam.aligned_sam_selector == '--sam' 78 #if $aligned_sam.aligned_sam_selector == '--sam'
76 $aligned_sam.sq 79 $aligned_sam.sq
77 #end if 80 #end if
78 $aligned_blast 81 #if $aligned_blast.aligned_blast_selector == '--blast'
82 --blast "$aligned_blast.aligned_blast_format"
83 #end if
79 84
80 $log 85 $log
81 86
82 #if $report.report_type == 'best' 87 #if $report.report_type == 'best'
83 #if $report.report_best.report_best_type == '1' 88 #if $report.report_best.report_best_type == '1'
113 </param> 118 </param>
114 <when value="not_paired" /> 119 <when value="not_paired" />
115 <when value="paired"> 120 <when value="paired">
116 <param name="paired_type" type="select" display="radio" label="If one of the paired-end reads aligns and the other one does not"> 121 <param name="paired_type" type="select" display="radio" label="If one of the paired-end reads aligns and the other one does not">
117 <option value="">leave the reads split between aligned and rejected files</option> 122 <option value="">leave the reads split between aligned and rejected files</option>
118 <option value="--paired-in">output both reads to aligned file (--paired-in)</option> 123 <option value="--paired_in">output both reads to aligned file (--paired_in)</option>
119 <option value="--paired-out">output both reads to rejected file (--paired-out)</option> 124 <option value="--paired_out">output both reads to rejected file (--paired_out)</option>
120 </param> 125 </param>
121 </when> 126 </when>
122 </conditional> 127 </conditional>
123 128
124 <param name="strand_search" type="select" label="Which strands to search"> 129 <param name="strand_search" type="select" label="Which strands to search">
177 <when value="--sam"> 182 <when value="--sam">
178 <param name="sq" type="boolean" truevalue="--SQ" falsevalue="" label="Add SQ tags to the SAM file" help="(--SQ)" /> 183 <param name="sq" type="boolean" truevalue="--SQ" falsevalue="" label="Add SQ tags to the SAM file" help="(--SQ)" />
179 </when> 184 </when>
180 <when value="" /> 185 <when value="" />
181 </conditional> 186 </conditional>
182 <param name="aligned_blast" type="select" label="Include alignments in BLAST-like format"> 187 <conditional name="aligned_blast">
183 <option value="--blast 0">pairwise (--blast 0)</option> 188 <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> 189 <option value="--blast">Yes</option>
185 <option value="--blast 2">tabular + column for CIGAR (--blast 2)</option> 190 <option value="" selected="true">No</option>
186 <option value="--blast 3">tabular + columns for CIGAR and query coverage (--blast 3)</option> 191 </param>
187 <option value="" selected="true">No</option> 192 <when value="--blast">
188 </param> 193 <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" 194 <option value="0">pairwise (--blast '0')</option>
195 <option value="1">tabular BLAST -m 8 format (--blast '1')</option>
196 <option value="1 cigar">tabular + column for CIGAR (--blast '1 cigar')</option>
197 <option value="1 cigar qcov">tabular + columns for CIGAR and query coverage (--blast '1 cigar qcov')</option>
198 <option value="1 cigar qcov qstrand">tabular + columns for CIGAR, query coverage and strand (--blast '1 cigar qcov qstrand')</option>
199 </param>
200 </when>
201 <when value="" />
202 </conditional>
203 <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)"> 204 help="Generates statistics for the rRNA content of reads, as well as rRNA subunit distribution. (--log)">
191 </param> 205 </param>
192 <conditional name="report"> 206 <conditional name="report">
193 <param name="report_type" type="select" label="Parameters for filtering and read mapping" help=""> 207 <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> 208 <option value="best" selected="true">Report best alignments per read reaching E-value</option>
245 label="Alignments on ${on_string} (SAM)"> 259 label="Alignments on ${on_string} (SAM)">
246 <filter>aligned_sam['aligned_sam_selector']</filter> 260 <filter>aligned_sam['aligned_sam_selector']</filter>
247 </data> 261 </data>
248 <data format="tabular" name="output_blast" from_work_dir="aligned.blast" 262 <data format="tabular" name="output_blast" from_work_dir="aligned.blast"
249 label="Alignments on ${on_string} (BLAST)"> 263 label="Alignments on ${on_string} (BLAST)">
250 <filter>aligned_blast</filter> 264 <filter>aligned_blast['aligned_blast_selector']</filter>
251 <change_format> 265 <change_format>
252 <when input="aligned_blast" value="--blast 0" format="txt" /> 266 <when input="aligned_blast.aligned_blast_format" value="0" format="txt" />
253 </change_format> 267 </change_format>
254 </data> 268 </data>
255 <data format="txt" name="output_log" label="${tool.name} statistics (txt)" from_work_dir="aligned.log"> 269 <data format="txt" name="output_log" label="${tool.name} statistics (txt)" from_work_dir="aligned.log">
256 <filter>log</filter> 270 <filter>log</filter>
257 </data> 271 </data>
261 <param name="input_reads" value="read_small.fastq" /> 275 <param name="input_reads" value="read_small.fastq" />
262 <param name="sequencing_type_selector" value="not_paired" /> 276 <param name="sequencing_type_selector" value="not_paired" />
263 <param name="strand_search" value="" /> 277 <param name="strand_search" value="" />
264 <param name="databases_selector" value="history" /> 278 <param name="databases_selector" value="history" />
265 <param name="database_name" value="ref_small.fasta" /> 279 <param name="database_name" value="ref_small.fasta" />
280 <param name="aligned_fastx_selector" value="--fastx" />
266 <param name="other" value="True" /> 281 <param name="other" value="True" />
282 <param name="aligned_sam_selector" value="--sam" />
283 <param name="aligned_blast_selector" value="--blast"/>
284 <param name="aligned_blast_format" value="1 cigar qcov" />
267 <param name="log" value="" /> 285 <param name="log" value="" />
286 <param name="report_type" value="best" />
287 <param name="report_best_type" value="1" />
288 <param name="e_value" value="1"/>
289 <param name="match" value="2"/>
290 <param name="mismatch" value="-3" />
291 <param name="gap_open" value="5"/>
292 <param name="gap_ext" value="2"/>
293 <param name="ambiguous_letter" value="-3"/>
268 <output name="output_fastx" file="sortmerna_wrapper_accept1.fastq" /> 294 <output name="output_fastx" file="sortmerna_wrapper_accept1.fastq" />
269 <output name="output_other" file="sortmerna_wrapper_other1.fastq" /> 295 <output name="output_other" file="sortmerna_wrapper_other1.fastq" />
270 <output name="output_sam" file="sortmerna_wrapper_sam1.sam" lines_diff="2" /> 296 <output name="output_sam" file="sortmerna_wrapper_sam1.sam" lines_diff="2" />
271 </test> 297 </test>
272 <test> 298 <test>
273 <param name="input_reads" value="read_small.fasta" /> 299 <param name="input_reads" value="read_small.fasta" />
274 <param name="sequencing_type_selector" value="not_paired" /> 300 <param name="sequencing_type_selector" value="not_paired" />
275 <param name="strand_search" value="" /> 301 <param name="strand_search" value="" />
276 <param name="databases_selector" value="history" /> 302 <param name="databases_selector" value="history" />
277 <param name="database_name" value="ref_small.fasta" /> 303 <param name="database_name" value="ref_small.fasta" />
304 <param name="aligned_fastx_selector" value="--fastx" />
278 <param name="other" value="True" /> 305 <param name="other" value="True" />
306 <param name="aligned_sam_selector" value="--sam" />
307 <param name="aligned_blast" value="" />
279 <param name="log" value="" /> 308 <param name="log" value="" />
309 <param name="report_type" value="best" />
310 <param name="report_best_type" value="1" />
311 <param name="report_type" value="best" />
312 <param name="report_best_type" value="1" />
313 <param name="e_value" value="1"/>
314 <param name="match" value="2"/>
315 <param name="mismatch" value="-3" />
316 <param name="gap_open" value="5"/>
317 <param name="gap_ext" value="2"/>
318 <param name="ambiguous_letter" value="-3"/>
280 <output name="output_fastx" file="sortmerna_wrapper_accept2.fasta" /> 319 <output name="output_fastx" file="sortmerna_wrapper_accept2.fasta" />
281 <output name="output_other" file="sortmerna_wrapper_other2.fasta" /> 320 <output name="output_other" file="sortmerna_wrapper_other2.fasta" />
282 <output name="output_sam" file="sortmerna_wrapper_sam2.sam" lines_diff="2" /> 321 <output name="output_sam" file="sortmerna_wrapper_sam2.sam" lines_diff="2" />
283 </test> 322 </test>
284 </tests> 323 </tests>