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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc
author rnateam
date Wed, 20 Mar 2019 03:00:33 -0400
parents 035f14f54ba7
children
comparison
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11:035f14f54ba7 12:67a87a218aa4
1 <tool id="bg_sortmerna" name="Filter with SortMeRNA" version="@VERSION@.4"> 1 <tool id="bg_sortmerna" name="Filter with SortMeRNA" version="@VERSION@.6">
2 <description>Fast and accurate filtering of ribosomal RNAs in metatranscriptomic data</description> 2 <description>of ribosomal RNAs in metatranscriptomic data</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <token name="@VERSION@">2.1b</token>
5 <xml name="db_prep">
6 <param name="seed_length" type="integer" min="0" max="100" value="18" label="Seed length for database indexing" help="(-L)"/>
7 <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 (--max_pos)"/>
8 </xml>
9 <xml name="output_alignments">
10 <param name="print_all_reads" type="boolean" checked="false" truevalue="--print_all_reads" falsevalue="" label="Output null alignment strings for non-aligned reads"/>
11 <conditional name="blast">
12 <param name="blast_output" type="select" label="Output BLAST report?">
13 <option value="True">Yes</option>
14 <option value="False" selected="True">No</option>
15 </param>
16 <when value="True">
17 <param name="blast_format" type="select" label="BLAST-like format?">
18 <option value="0">pairwise (--blast '0')</option>
19 <option value="1">tabular BLAST -m 8 format (--blast '1')</option>
20 <option value="1 cigar">tabular + column for CIGAR (--blast '1 cigar')</option>
21 <option value="1 cigar qcov">tabular + columns for CIGAR and query coverage (--blast '1 cigar qcov')</option>
22 <option value="1 cigar qcov qstrand">tabular + columns for CIGAR, query coverage and strand (--blast '1 cigar qcov qstrand')</option>
23 </param>
24 </when>
25 <when value="False"/>
26 </conditional>
27 </xml>
28 <token name="@ALIGNMENTS@">
29 $report.print_all_reads
30 --sam
31 --SQ
32 #if $report.blast.blast_output == 'True'
33 --blast '$report.blast.blast_format'
34 #end if
35 </token>
5 </macros> 36 </macros>
6 <requirements> 37 <requirements>
7 <requirement type="package" version="@VERSION@">sortmerna</requirement> 38 <requirement type="package" version="@VERSION@">sortmerna</requirement>
39 <requirement type="package" version="1.5">samtools</requirement>
8 </requirements> 40 </requirements>
9 <stdio> 41 <stdio>
10 <regex match="This program builds a Burst trie on an input rRNA database" 42 <regex match="This program builds a Burst trie on an input rRNA database"
11 source="both" 43 source="both"
12 level="fatal" 44 level="fatal"
44 #set $ref += $sep + $db + ',' + $os.path.splitext($db)[0] 76 #set $ref += $sep + $db + ',' + $os.path.splitext($db)[0]
45 #set $sep = ':' 77 #set $sep = ':'
46 #end for 78 #end for
47 #end if 79 #end if
48 80
49 #if str( $databases_type.databases_selector ) != 'cached': 81 #if str( $databases_type.databases_selector ) != 'cached'
50 indexdb_rna 82 indexdb_rna
51 --ref $ref 83 --ref '$ref'
52 -L $databases_type.seed_length 84 -L '$databases_type.seed_length'
53 --max_pos $databases_type.max_pos 85 --max_pos '$databases_type.max_pos'
54 && 86 &&
55 #end if 87 #end if
56 88
89 #if str( $sequencing_type.sequencing_type_selector ) == 'paired'
90 merge-paired-reads.sh
91 '$sequencing_type.forward_reads'
92 '$sequencing_type.reverse_reads'
93 merged-reads
94 &&
95 #end if
96
57 sortmerna 97 sortmerna
58 --ref $ref 98 --ref '$ref'
59 --reads $input_reads 99 --aligned 'aligned'
60 --aligned aligned 100 #if str( $sequencing_type.sequencing_type_selector ) == 'paired'
61 101 --reads 'merged-reads'
62 #if str( $sequencing_type.sequencing_type_selector ) == 'paired' 102 $sequencing_type.paired_type
63 $sequencing_type.paired_type 103 #else
64 #end if 104 --reads '$sequencing_type.reads'
65 105 #end if
66 $strand_search 106 $strand_search
67 $aligned_fastx.aligned_fastx_selector 107 $log
68 #if $aligned_fastx.aligned_fastx_selector == '--fastx' 108 $aligned_fastx.aligned_fastx_selector
69 #if $aligned_fastx.other 109 #if $aligned_fastx.aligned_fastx_selector == '--fastx'
70 --other other_file 110 #if $aligned_fastx.other
71 #end if 111 --other 'unaligned'
72 #end if 112 #end if
73 $aligned_sam.aligned_sam_selector 113 #end if
74 #if $aligned_sam.aligned_sam_selector == '--sam'
75 $aligned_sam.sq
76 #end if
77 #if $aligned_blast.aligned_blast_selector == '--blast'
78 --blast "$aligned_blast.aligned_blast_format"
79 #end if
80
81 $log
82
83 #if $report.report_type == 'best' 114 #if $report.report_type == 'best'
115 @ALIGNMENTS@
116 #if $report.otu.otu_map == 'True'
117 --otu_map
118 --id '$report.otu.id'
119 --coverage '$report.otu.coverage'
120 $report.otu.de_novo_otu
121 #end if
84 #if $report.report_best.report_best_type == '1' 122 #if $report.report_best.report_best_type == '1'
85 --best 1 123 --best 1
86 --min_lis $report.report_best.report_best_min_lis 124 --min_lis '$report.report_best.report_best_min_lis'
87 #else 125 #else
88 --best $report.report_best.report_best_value 126 --best '$report.report_best.report_best_value'
89 --min_lis $report.report_best.report_best_min_lis 127 --min_lis '$report.report_best.report_best_min_lis'
128 #end if
129 #elif $report.report_type == 'num_alignments'
130 @ALIGNMENTS@
131 #if $report.report_num_alignments.report_num_alignments_type == 'other_value'
132 --num_alignments '$report.report_num_alignments.report_num_alignments_value'
133 #else
134 --num_alignments '$report.report_num_alignments.report_num_alignments_type'
135 #end if
136 #end if
137 -e '$e_value'
138 --match '$match'
139 --mismatch '$mismatch'
140 --gap_open '$gap_open'
141 --gap_ext '$gap_ext'
142 -N '$ambiguous_letter'
143 -a \${GALAXY_SLOTS:-1}
144 #if $report.report_type != 'None'
145 &&
146 samtools view -@ "\${GALAXY_SLOTS:-4}" -u aligned.sam | samtools sort -@ "\${GALAXY_SLOTS:-4}" -T tmp -O bam -o '$output_bam'
147 #end if
148
149 #if $aligned_fastx.aligned_fastx_selector == '--fastx' and str($sequencing_type.sequencing_type_selector) == 'paired'
150 #if str($sequencing_type.paired_type) != ''
151 &&
152 unmerge-paired-reads.sh
153 aligned.fast*
154 '$aligned_forward'
155 '$aligned_reverse'
156 #if $aligned_fastx.other
157 &&
158 unmerge-paired-reads.sh
159 unaligned.fast*
160 '$unaligned_forward'
161 '$unaligned_reverse'
90 #end if 162 #end if
91 #else 163 #else
92 #if $report.report_num_alignments.report_num_alignments_type == 'other_value' 164 &&
93 --num_alignments $report.report_num_alignments.report_num_alignments_value 165 mv aligned.fast* '$aligned_paired'
94 #else 166 #if $aligned_fastx.other
95 --num_alignments $report.report_num_alignments.report_num_alignments_type 167 &&
168 mv unaligned.fast* '$unaligned_paired'
96 #end if 169 #end if
97 #end if 170 #end if
98 171 #end if
99 -e $e_value
100 --match $match
101 --mismatch $mismatch
102 --gap_open $gap_open
103 --gap_ext $gap_ext
104 -N $ambiguous_letter
105 -a \${GALAXY_SLOTS:-1}
106 ]]> 172 ]]>
107 </command> 173 </command>
108 <inputs> 174 <inputs>
109 <param format="fasta,fastq" name="input_reads" type="data" label="Querying sequences" help="In FASTA or FASTQ format (--reads)"/>
110 <conditional name="sequencing_type"> 175 <conditional name="sequencing_type">
111 <param name="sequencing_type_selector" type="select" label="Sequencing type"> 176 <param name="sequencing_type_selector" type="select" label="Sequencing type">
112 <option value="not_paired">Reads are not paired</option> 177 <option value="not_paired">Reads are not paired</option>
113 <option value="paired">Reads are paired</option> 178 <option value="paired">Reads are paired</option>
114 </param> 179 </param>
115 <when value="not_paired" /> 180 <when value="not_paired">
181 <param argument="--reads" type="data" format="fasta,fastq" label="Querying sequences"/>
182 </when>
116 <when value="paired"> 183 <when value="paired">
184 <param name="forward_reads" type="data" format="fasta,fastq" label="Forward reads"/>
185 <param name="reverse_reads" type="data" format="fasta,fastq" label="Reverse reads"/>
117 <param name="paired_type" type="select" display="radio" label="If one of the paired-end reads aligns and the other one does not"> 186 <param name="paired_type" type="select" display="radio" label="If one of the paired-end reads aligns and the other one does not">
118 <option value="">leave the reads split between aligned and rejected files</option> 187 <option value="">Leave the reads split between aligned and rejected files</option>
119 <option value="--paired_in">output both reads to aligned file (--paired_in)</option> 188 <option value="--paired_in">Output both reads to aligned file (--paired_in)</option>
120 <option value="--paired_out">output both reads to rejected file (--paired_out)</option> 189 <option value="--paired_out">Output both reads to rejected file (--paired_out)</option>
121 </param> 190 </param>
122 </when> 191 </when>
123 </conditional> 192 </conditional>
124
125 <param name="strand_search" type="select" label="Which strands to search"> 193 <param name="strand_search" type="select" label="Which strands to search">
126 <option value="">Search both strands</option> 194 <option value="">Search both strands</option>
127 <option value="-F">Search only the forward strand (-F)</option> 195 <option value="-F">Search only the forward strand (-F)</option>
128 <option value="-R">Search only the reverse-complementary strand (-R)</option> 196 <option value="-R">Search only the reverse-complementary strand (-R)</option>
129 </param> 197 </param>
130
131 <conditional name="databases_type"> 198 <conditional name="databases_type">
132 <param name="databases_selector" type="select" label="Databases to query" 199 <param name="databases_selector" type="select" label="Databases to query"
133 help="Public rRNA databases provided with SortMeRNA have been indexed. 200 help="Public rRNA databases provided with SortMeRNA have been indexed. On the contrary, personal databases must be indexed each time SortMeRNA is launched. Please be patient, this may take some time depending on the size of the given database.">
134 On the contrary, personal databases must be indexed each time SortMeRNA is launched.
135 Please be patient, this may take some time depending on the size of the given database.">
136 <option value="cached" selected="true">Public pre-indexed ribosomal databases</option> 201 <option value="cached" selected="true">Public pre-indexed ribosomal databases</option>
137 <option value="cached_to_index">Public ribosomal databases to index with non default parameters</option> 202 <option value="cached_to_index">Public ribosomal databases to index with non default parameters</option>
138 <option value="history">Databases from your history</option> 203 <option value="history">Databases from your history</option>
139 </param> 204 </param>
140 <when value="cached"> 205 <when value="cached">
146 <when value="cached_to_index"> 211 <when value="cached_to_index">
147 <param name="input_databases" label="rRNA databases" type="select" display="checkboxes" multiple="true"> 212 <param name="input_databases" label="rRNA databases" type="select" display="checkboxes" multiple="true">
148 <options from_data_table="rRNA_databases" /> 213 <options from_data_table="rRNA_databases" />
149 <validator type="no_options" message="Select at least one database"/> 214 <validator type="no_options" message="Select at least one database"/>
150 </param> 215 </param>
151 <param name="seed_length" type="integer" min="0" max="100" value="18" label="Seed length for database indexing" help="(-L)"/> 216 <expand macro="db_prep"/>
152 <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 (--max_pos)"/>
153 </when> 217 </when>
154 <when value="history"> 218 <when value="history">
155 <param name="database_name" type="data" format="fasta" multiple="true" label="rRNA databases" 219 <param name="database_name" type="data" format="fasta" multiple="true" label="rRNA databases" help="Your databases will be indexed first, which may take up to several minutes."/>
156 help="Your databases will be indexed first, which may take up to several minutes."/> 220 <expand macro="db_prep"/>
157 <param name="seed_length" type="integer" min="0" max="100" value="18" label="Seed length for database indexing" help="(-L)"/>
158 <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 (--max_pos)"/>
159 </when> 221 </when>
160 </conditional> 222 </conditional>
161
162 <!-- Outputs --> 223 <!-- Outputs -->
163 <conditional name="aligned_fastx"> 224 <conditional name="aligned_fastx">
164 <param name="aligned_fastx_selector" type="select" label="Include aligned reads in FASTA/FASTQ format?"> 225 <param name="aligned_fastx_selector" type="select" label="Include aligned reads in FASTA/FASTQ format?">
165 <option value="--fastx">Yes (--fastx)</option> 226 <option value="--fastx">Yes (--fastx)</option>
166 <option value="">No</option> 227 <option value="">No</option>
167 </param> 228 </param>
168 <when value="--fastx"> 229 <when value="--fastx">
169 <param name="other" type="boolean" label="Include rejected reads file?" help="(--other)" /> 230 <param argument="--other" type="boolean" truevalue="True" falsevalue="False" label="Include rejected reads file?"/>
170 </when> 231 </when>
171 <when value="" /> 232 <when value=""/>
172 </conditional> 233 </conditional>
173 <conditional name="aligned_sam"> 234 <param argument="--log" type="boolean" checked="false" truevalue="--log" falsevalue="" label="Generate statistics file" help="Generates statistics for the rRNA content of reads, as well as rRNA subunit distribution">
174 <param name="aligned_sam_selector" type="select" label="Include alignments in SAM format?">
175 <option value="--sam">Yes (--sam)</option>
176 <option value="">No</option>
177 </param>
178 <when value="--sam">
179 <param name="sq" type="boolean" truevalue="--SQ" falsevalue="" label="Add SQ tags to the SAM file" help="(--SQ)" />
180 </when>
181 <when value="" />
182 </conditional>
183 <conditional name="aligned_blast">
184 <param name="aligned_blast_selector" type="select" label="Include alignments in BLAST-like format?">
185 <option value="--blast">Yes</option>
186 <option value="" selected="true">No</option>
187 </param>
188 <when value="--blast">
189 <param name="aligned_blast_format" type="select" label="BLAST-like format?">
190 <option value="0">pairwise (--blast '0')</option>
191 <option value="1">tabular BLAST -m 8 format (--blast '1')</option>
192 <option value="1 cigar">tabular + column for CIGAR (--blast '1 cigar')</option>
193 <option value="1 cigar qcov">tabular + columns for CIGAR and query coverage (--blast '1 cigar qcov')</option>
194 <option value="1 cigar qcov qstrand">tabular + columns for CIGAR, query coverage and strand (--blast '1 cigar qcov qstrand')</option>
195 </param>
196 </when>
197 <when value="" />
198 </conditional>
199 <param name="log" type="boolean" checked="false" truevalue="--log" falsevalue="" label="Generate statistics file"
200 help="Generates statistics for the rRNA content of reads, as well as rRNA subunit distribution. (--log)">
201 </param> 235 </param>
202 <conditional name="report"> 236 <conditional name="report">
203 <param name="report_type" type="select" label="Parameters for filtering and read mapping" help=""> 237 <param name="report_type" type="select" label="Alignment report">
204 <option value="best" selected="true">Report best alignments per read reaching E-value</option> 238 <option value="None">Do not report alignments</option>
239 <option value="best">Report best alignments per read reaching E-value</option>
205 <option value="num_alignments">Report first alignements per read reaching E-value</option> 240 <option value="num_alignments">Report first alignements per read reaching E-value</option>
206 </param> 241 </param>
242 <when value="None"/>
207 <when value="best"> 243 <when value="best">
244 <expand macro="output_alignments"/>
245 <conditional name="otu">
246 <param name="otu_map" type="select" label="Pick OTUs?">
247 <option value="True">Yes</option>
248 <option value="False" selected="true">No</option>
249 </param>
250 <when value="True">
251 <param argument="--id" type="float" value="0.97" label="Percentage id similarity threshold" help="The alignment must still pass the E-value threshold" />
252 <param argument="--coverage" type="float" value="0.97" label="Percentage query coverage threshold" help="The alignment must still pass the E-value threshold" />
253 <param name="de_novo_otu" type="boolean" truevalue="--de_novo_otu" falsevalue="" label="FASTA/FASTQ file for reads matching database below percentage id" help="--de_novo_otu" />
254 </when>
255 <when value="False"/>
256 </conditional>
208 <conditional name="report_best"> 257 <conditional name="report_best">
209 <param name="report_best_type" type="select" label="Number of searched alignments" help="Only the best alignment is reported (--best)"> 258 <param argument="report_best_type" type="select" label="Number of searched alignments" help="Only the best alignment is reported (--best)">
210 <option value="1" selected="true">Only one high-candidate reference sequence is searched for alignments (fast). The high-candidate sequences are determined heuristically using a LIS of seed matches)</option> 259 <option value="1" selected="true">Only one high-candidate reference sequence is searched for alignments (fast). The high-candidate sequences are determined heuristically using a LIS of seed matches)</option>
211 <option value="other_value">A custom number of reference sequences are searched for alignments (speed decrease for high value)</option> 260 <option value="other_value">A custom number of reference sequences are searched for alignments (speed decrease for high value)</option>
212 </param> 261 </param>
213 <when value="1"> 262 <when value="1">
214 <param name="report_best_min_lis" type="integer" min="0" max="100" value="2" label="Number of longest LIS an alignement needs to be searched" help="The alignements having the first INT longest LIS. LIS stands for Longest Increasing Subsequence, it is computed using seeds' positions to expand hits into longer matches prior to Smith-Waterman alignment. (--min_lis)"/> 263 <param name="report_best_min_lis" type="integer" min="0" max="100" value="2" label="Number of longest LIS an alignement needs to be searched" help="The alignements having the first INT longest LIS. LIS stands for Longest Increasing Subsequence, it is computed using seeds' positions to expand hits into longer matches prior to Smith-Waterman alignment. (--min_lis)"/>
218 <param name="report_best_min_lis" type="integer" min="0" max="100" value="2" label="Number of longest LIS an alignement needs to be searched" help="The alignements having the first INT longest LIS. LIS stands for Longest Increasing Subsequence, it is computed using seeds' positions to expand hits into longer matches prior to Smith-Waterman alignment. (--min_lis)"/> 267 <param name="report_best_min_lis" type="integer" min="0" max="100" value="2" label="Number of longest LIS an alignement needs to be searched" help="The alignements having the first INT longest LIS. LIS stands for Longest Increasing Subsequence, it is computed using seeds' positions to expand hits into longer matches prior to Smith-Waterman alignment. (--min_lis)"/>
219 </when> 268 </when>
220 </conditional> 269 </conditional>
221 </when> 270 </when>
222 <when value="num_alignments"> 271 <when value="num_alignments">
272 <expand macro="output_alignments"/>
223 <conditional name="report_num_alignments"> 273 <conditional name="report_num_alignments">
224 <param name="report_num_alignments_type" type="select" label="Number of output alignments" help="(--num_alignments)"> 274 <param name="report_num_alignments_type" type="select" label="Number of output alignments" help="(--num_alignments)">
225 <option value="0">All alignments reaching the E-value threshold are reported (very slow, this option is not suggested for high similarity rRNA databases)</option> 275 <option value="0">All alignments reaching the E-value threshold are reported (very slow, this option is not suggested for high similarity rRNA databases)</option>
226 <option value="1" selected="true">The first alignment passing E-value threshold are reported (very fast, best choice if only filtering is needed)</option> 276 <option value="1" selected="true">The first alignment passing E-value threshold are reported (very fast, best choice if only filtering is needed)</option>
227 <option value="other_value">A custom number of alignments are made and reported (speed decrease for high value)</option> 277 <option value="other_value">A custom number of alignments are made and reported (speed decrease for high value)</option>
232 <param name="report_num_alignments_value" type="integer" min="0" max="100" value="1" label="Number of alignments to be made and reported" help=""/> 282 <param name="report_num_alignments_value" type="integer" min="0" max="100" value="1" label="Number of alignments to be made and reported" help=""/>
233 </when> 283 </when>
234 </conditional> 284 </conditional>
235 </when> 285 </when>
236 </conditional> 286 </conditional>
237
238 <param name="e_value" type="float" min="0" max="10" value="1" label="E-value threshold" help="(-e)"/> 287 <param name="e_value" type="float" min="0" max="10" value="1" label="E-value threshold" help="(-e)"/>
239 <param name="match" type="integer" min="0" max="10" value="2" label="SW score for a match" help="(--match)"/> 288 <param argument="--match" type="integer" min="0" max="10" value="2" label="SW score for a match"/>
240 <param name="mismatch" type="integer" min="-10" max="0" value="-3" label="SW penalty for a mismatch" help="(--mismatch)"/> 289 <param argument="--mismatch" type="integer" min="-10" max="0" value="-3" label="SW penalty for a mismatch"/>
241 <param name="gap_open" type="integer" min="0" max="10" value="5" label="SW penalty for introducing a gap" help="(--gap_open)"/> 290 <param name="gap_open" type="integer" min="0" max="10" value="5" label="SW penalty for introducing a gap" help="(--gap_open)"/>
242 <param name="gap_ext" type="integer" min="0" max="10" value="2" label="SW penalty for extending a gap" help="(--gap_ext)"/> 291 <param name="gap_ext" type="integer" min="0" max="10" value="2" label="SW penalty for extending a gap" help="(--gap_ext)"/>
243 <param name="ambiguous_letter" type="integer" min="-10" max="0" value="-3" label="SW penalty for ambiguous letters (N's)" help="(-N)"/> 292 <param name="ambiguous_letter" type="integer" min="-10" max="0" value="-3" label="SW penalty for ambiguous letters (N's)" help="(-N)"/>
244 </inputs> 293 </inputs>
245 <outputs> 294 <outputs>
246 <data format_source="input_reads" name="output_fastx" from_work_dir="aligned.dat" 295 <data name="output_fastx" format_source="reads" from_work_dir="aligned.dat" label="${tool.name} on ${on_string}: Aligned reads">
247 label="Aligned reads on ${on_string} (${input_reads.datatype.file_ext})"> 296 <filter>aligned_fastx['aligned_fastx_selector'] != '' and sequencing_type['sequencing_type_selector'] != 'paired'</filter>
248 <filter>aligned_fastx['aligned_fastx_selector']</filter> 297 </data>
249 </data> 298 <data name="aligned_paired" format_source="forward_reads" label="${tool.name} on ${on_string}: Aligned reads">
250 <data format_source="input_reads" name="output_other" from_work_dir="other_file.dat" 299 <filter>aligned_fastx['aligned_fastx_selector'] != '' and sequencing_type['sequencing_type_selector'] == 'paired' and sequencing_type['paired_type'] == ''</filter>
251 label="Rejected reads on ${on_string} (${input_reads.datatype.file_ext})"> 300 </data>
252 <filter>aligned_fastx['aligned_fastx_selector'] and aligned_fastx['other']</filter> 301 <data name="aligned_forward" format_source="forward_reads" label="${tool.name} on ${on_string}: Aligned forward reads">
253 </data> 302 <filter>aligned_fastx['aligned_fastx_selector'] != '' and sequencing_type['sequencing_type_selector'] == 'paired' and sequencing_type['paired_type'] != ''</filter>
254 <data format="sam" name="output_sam" from_work_dir="aligned.sam" 303 </data>
255 label="Alignments on ${on_string} (SAM)"> 304 <data name="aligned_reverse" format_source="reverse_reads" label="${tool.name} on ${on_string}: Aligned reverse reads">
256 <filter>aligned_sam['aligned_sam_selector']</filter> 305 <filter>aligned_fastx['aligned_fastx_selector'] != '' and sequencing_type['sequencing_type_selector'] == 'paired' and sequencing_type['paired_type'] != ''</filter>
257 </data> 306 </data>
258 <data format="tabular" name="output_blast" from_work_dir="aligned.blast" 307 <data name="output_other" format_source="reads" from_work_dir="unaligned.dat" label="${tool.name} on ${on_string}: Unaligned reads">
259 label="Alignments on ${on_string} (BLAST)"> 308 <filter>aligned_fastx['aligned_fastx_selector'] != '' and aligned_fastx['other'] == True and sequencing_type['sequencing_type_selector'] != 'paired'</filter>
260 <filter>aligned_blast['aligned_blast_selector']</filter> 309 </data>
310 <data name="unaligned_paired" format_source="forward_reads" label="${tool.name} on ${on_string}: Unaligned reads">
311 <filter>aligned_fastx['aligned_fastx_selector'] != '' and aligned_fastx['other'] == True and sequencing_type['sequencing_type_selector'] == 'paired' and sequencing_type['paired_type'] == ''</filter>
312 </data>
313 <data name="unaligned_forward" format_source="forward_reads" label="${tool.name} on ${on_string}: Unaligned forward reads">
314 <filter>aligned_fastx['aligned_fastx_selector'] != '' and aligned_fastx['other'] == True and sequencing_type['sequencing_type_selector'] == 'paired' and sequencing_type['paired_type'] != ''</filter>
315 </data>
316 <data name="unaligned_reverse" format_source="reverse_reads" label="${tool.name} on ${on_string}: Unaligned reverse reads">
317 <filter>aligned_fastx['aligned_fastx_selector'] != '' and aligned_fastx['other'] == True and sequencing_type['sequencing_type_selector'] == 'paired' and sequencing_type['paired_type'] != ''</filter>
318 </data>
319 <data name="output_bam" format="bam" label="${tool.name} on ${on_string}: Alignments">
320 <filter>report['report_type'] != 'None'</filter>
321 </data>
322 <data name="output_blast" format="tabular" from_work_dir="aligned.blast" label="${tool.name} on ${on_string}: BLAST report">
323 <filter>report['report_type'] != 'None' and report['blast']['blast_output'] == 'True'</filter>
261 <change_format> 324 <change_format>
262 <when input="aligned_blast.aligned_blast_format" value="0" format="txt" /> 325 <when input="aligned_blast.aligned_blast_format" value="0" format="txt" />
263 </change_format> 326 </change_format>
264 </data> 327 </data>
265 <data format="txt" name="output_log" label="${tool.name} statistics (txt)" from_work_dir="aligned.log"> 328 <data name="output_biom" format="txt" from_work_dir="aligned_otus.txt" label="${tool.name} on ${on_string}: OTU map">
266 <filter>log</filter> 329 <filter>report['report_type'] != 'None' and report['report_type'] == 'best' and report['otu']['otu_map'] == 'True'</filter>
330 </data>
331 <data name="output_de_novo" format_source="reads" from_work_dir="aligned_denovo.dat" label="${tool.name} on ${on_string}: De novo reads matching database">
332 <filter>report['report_type'] != 'None' and report['report_type'] == 'best' and report['otu']['otu_map'] == 'True' and report['otu']['de_novo_otu'] == True</filter>
333 </data>
334 <data name="output_log" format="txt" label="${tool.name} on ${on_string}: Log" from_work_dir="aligned.log">
335 <filter>log == True</filter>
267 </data> 336 </data>
268 </outputs> 337 </outputs>
269 <tests> 338 <tests>
270 <test> 339 <test>
271 <param name="input_reads" value="read_small.fastq" /> 340 <conditional name="sequencing_type">
272 <param name="sequencing_type_selector" value="not_paired" /> 341 <param name="sequencing_type_selector" value="not_paired" />
342 <param name="reads" value="read_small.fastq" />
343 </conditional>
273 <param name="strand_search" value="" /> 344 <param name="strand_search" value="" />
274 <param name="databases_selector" value="history" /> 345 <conditional name="databases_type">
275 <param name="database_name" value="ref_small.fasta" /> 346 <param name="databases_selector" value="history" />
276 <param name="aligned_fastx_selector" value="--fastx" /> 347 <param name="database_name" value="ref_small.fasta" />
277 <param name="other" value="True" /> 348 </conditional>
278 <param name="aligned_sam_selector" value="--sam" /> 349 <conditional name="aligned_fastx">
279 <param name="aligned_blast_selector" value="--blast"/> 350 <param name="aligned_fastx_selector" value="--fastx" />
280 <param name="aligned_blast_format" value="1 cigar qcov" /> 351 <param name="other" value="True" />
281 <param name="log" value="" /> 352 </conditional>
282 <param name="report_type" value="best" /> 353 <param name="log" value="False" />
283 <param name="report_best_type" value="1" /> 354 <conditional name="report">
355 <param name="report_type" value="num_alignments" />
356 <param name="report_best_type" value="1" />
357 <param name="print_all_reads" value="False" />
358 <conditional name="blast">
359 <param name="blast_output" value="True"/>
360 <param name="blast_format" value="1 cigar qcov"/>
361 </conditional>
362 <conditional name="otu">
363 <param name="otu_map" value="False"/>
364 </conditional>
365 </conditional>
284 <param name="e_value" value="1"/> 366 <param name="e_value" value="1"/>
285 <param name="match" value="2"/> 367 <param name="match" value="2"/>
286 <param name="mismatch" value="-3" /> 368 <param name="mismatch" value="-3" />
287 <param name="gap_open" value="5"/> 369 <param name="gap_open" value="5"/>
288 <param name="gap_ext" value="2"/> 370 <param name="gap_ext" value="2"/>
289 <param name="ambiguous_letter" value="-3"/> 371 <param name="ambiguous_letter" value="-3"/>
290 <output name="output_fastx" file="sortmerna_wrapper_accept1.fastq" /> 372 <output name="output_fastx" file="test1_aligned.fastq" />
291 <output name="output_other" file="sortmerna_wrapper_other1.fastq" /> 373 <output name="output_other" file="test1_other.fastq" />
292 <output name="output_sam" file="sortmerna_wrapper_sam1.sam" lines_diff="2" /> 374 <output name="output_bam" file="test1_bam.bam" compare="sim_size" delta="200" />
375 <output name="output_blast" file="test1_blast.tabular"/>
293 </test> 376 </test>
294 <test> 377 <test>
295 <param name="input_reads" value="read_small.fasta" /> 378 <conditional name="sequencing_type">
296 <param name="sequencing_type_selector" value="not_paired" /> 379 <param name="sequencing_type_selector" value="not_paired" />
380 <param name="reads" value="read_small.fasta" />
381 </conditional>
297 <param name="strand_search" value="" /> 382 <param name="strand_search" value="" />
298 <param name="databases_selector" value="history" /> 383 <conditional name="databases_type">
299 <param name="database_name" value="ref_small.fasta" /> 384 <param name="databases_selector" value="history" />
300 <param name="aligned_fastx_selector" value="--fastx" /> 385 <param name="database_name" value="ref_small.fasta" />
301 <param name="other" value="True" /> 386 </conditional>
302 <param name="aligned_sam_selector" value="--sam" /> 387 <conditional name="aligned_fastx">
303 <param name="aligned_blast" value="" /> 388 <param name="aligned_fastx_selector" value="--fastx" />
304 <param name="log" value="" /> 389 <param name="other" value="False" />
305 <param name="report_type" value="best" /> 390 </conditional>
306 <param name="report_best_type" value="1" /> 391 <param name="log" value="True" />
307 <param name="report_type" value="best" /> 392 <conditional name="report">
308 <param name="report_best_type" value="1" /> 393 <param name="report_type" value="None" />
394 </conditional>
309 <param name="e_value" value="1"/> 395 <param name="e_value" value="1"/>
310 <param name="match" value="2"/> 396 <param name="match" value="2"/>
311 <param name="mismatch" value="-3" /> 397 <param name="mismatch" value="-3" />
312 <param name="gap_open" value="5"/> 398 <param name="gap_open" value="5"/>
313 <param name="gap_ext" value="2"/> 399 <param name="gap_ext" value="2"/>
314 <param name="ambiguous_letter" value="-3"/> 400 <param name="ambiguous_letter" value="-3"/>
315 <output name="output_fastx" file="sortmerna_wrapper_accept2.fasta" /> 401 <output name="output_fastx" file="test2_aligned.fasta" />
316 <output name="output_other" file="sortmerna_wrapper_other2.fasta" /> 402 <output name="output_log" file="test2_log.txt" compare="sim_size" />
317 <output name="output_sam" file="sortmerna_wrapper_sam2.sam" lines_diff="2" /> 403 </test>
404 <test>
405 <conditional name="sequencing_type">
406 <param name="sequencing_type_selector" value="paired" />
407 <param name="forward_reads" value="forward_reads.fastq" />
408 <param name="reverse_reads" value="reverse_reads.fastq" />
409 <param name="paired_type" value="--paired_in"/>
410 </conditional>
411 <param name="strand_search" value="" />
412 <conditional name="databases_type">
413 <param name="databases_selector" value="history" />
414 <param name="database_name" value="ref_small.fasta" />
415 <param name="seed_length" value="18" />
416 <param name="max_pos" value="100000"/>
417 </conditional>
418 <conditional name="aligned_fastx">
419 <param name="aligned_fastx_selector" value="--fastx" />
420 <param name="other" value="True" />
421 </conditional>
422 <param name="log" value="False" />
423 <conditional name="report">
424 <param name="report_type" value="best" />
425 <param name="report_num_alignments_type" value="1"/>
426 <param name="print_all_reads" value="False" />
427 <conditional name="blast">
428 <param name="blast_output" value="False"/>
429 </conditional>
430 <conditional name="otu">
431 <param name="otu_map" value="False"/>
432 </conditional>
433 </conditional>
434 <param name="e_value" value="1"/>
435 <param name="match" value="2"/>
436 <param name="mismatch" value="-3" />
437 <param name="gap_open" value="5"/>
438 <param name="gap_ext" value="2"/>
439 <param name="ambiguous_letter" value="-3"/>
440 <output name="aligned_forward" file="test3_aligned_forward.fastq" />
441 <output name="aligned_reverse" file="test3_aligned_reverse.fastq" />
442 <output name="unaligned_forward" file="test3_unaligned_forward.fastq" />
443 <output name="unaligned_reverse" file="test3_unaligned_reverse.fastq" />
444 <output name="output_bam" file="test3_bam.bam" compare="sim_size" delta="200" />
445 </test>
446 <test>
447 <conditional name="sequencing_type">
448 <param name="sequencing_type_selector" value="not_paired" />
449 <param name="reads" value="test4_input.fasta" />
450 </conditional>
451 <param name="strand_search" value="" />
452 <conditional name="databases_type">
453 <param name="databases_selector" value="history" />
454 <param name="database_name" value="ref_small.fasta" />
455 <param name="seed_length" value="18" />
456 <param name="max_pos" value="100000"/>
457 </conditional>
458 <conditional name="aligned_fastx">
459 <param name="aligned_fastx_selector" value="" />
460 </conditional>
461 <param name="log" value="False" />
462 <conditional name="report">
463 <param name="report_type" value="best" />
464 <param name="report_num_alignments_type" value="1"/>
465 <param name="print_all_reads" value="False" />
466 <conditional name="blast">
467 <param name="blast_output" value="False"/>
468 </conditional>
469 <conditional name="otu">
470 <param name="otu_map" value="True"/>
471 <param name="id" value="0.97"/>
472 <param name="coverage" value="0.97" />
473 <param name="de_novo_otu" value="True"/>
474 </conditional>
475 </conditional>
476 <param name="e_value" value="1"/>
477 <param name="match" value="2"/>
478 <param name="mismatch" value="-3" />
479 <param name="gap_open" value="5"/>
480 <param name="gap_ext" value="2"/>
481 <param name="ambiguous_letter" value="-3"/>
482 <output name="output_bam" file="test4_bam.bam" compare="sim_size" delta="200" />
483 <output name="output_biom" file="test4_biom.txt"/>
484 <output name="output_de_novo" file="test4_de_novo.fasta"/>
485 </test>
486 <test>
487 <conditional name="sequencing_type">
488 <param name="sequencing_type_selector" value="paired" />
489 <param name="forward_reads" value="forward_reads.fasta" />
490 <param name="reverse_reads" value="reverse_reads.fasta" />
491 <param name="paired_type" value=""/>
492 </conditional>
493 <param name="strand_search" value="" />
494 <conditional name="databases_type">
495 <param name="databases_selector" value="history" />
496 <param name="database_name" value="ref_small.fasta" />
497 <param name="seed_length" value="18" />
498 <param name="max_pos" value="100000"/>
499 </conditional>
500 <conditional name="aligned_fastx">
501 <param name="aligned_fastx_selector" value="--fastx" />
502 <param name="other" value="True" />
503 </conditional>
504 <param name="log" value="False" />
505 <conditional name="report">
506 <param name="report_type" value="best" />
507 <param name="report_num_alignments_type" value="1"/>
508 <param name="print_all_reads" value="False" />
509 <conditional name="blast">
510 <param name="blast_output" value="False"/>
511 </conditional>
512 <conditional name="otu">
513 <param name="otu_map" value="False"/>
514 </conditional>
515 </conditional>
516 <param name="e_value" value="1"/>
517 <param name="match" value="2"/>
518 <param name="mismatch" value="-3" />
519 <param name="gap_open" value="5"/>
520 <param name="gap_ext" value="2"/>
521 <param name="ambiguous_letter" value="-3"/>
522 <output name="aligned_paired" file="test5_aligned.fasta" />
523 <output name="unaligned_paired" file="test5_unaligned.fasta" />
524 </test>
525 <test>
526 <conditional name="sequencing_type">
527 <param name="sequencing_type_selector" value="paired" />
528 <param name="forward_reads" value="forward_reads.fasta" />
529 <param name="reverse_reads" value="reverse_reads.fasta" />
530 <param name="paired_type" value="--paired_out"/>
531 </conditional>
532 <param name="strand_search" value="" />
533 <conditional name="databases_type">
534 <param name="databases_selector" value="history" />
535 <param name="database_name" value="ref_small.fasta" />
536 <param name="seed_length" value="18" />
537 <param name="max_pos" value="100000"/>
538 </conditional>
539 <conditional name="aligned_fastx">
540 <param name="aligned_fastx_selector" value="--fastx" />
541 <param name="other" value="True" />
542 </conditional>
543 <param name="log" value="False" />
544 <conditional name="report">
545 <param name="report_type" value="best" />
546 <param name="report_num_alignments_type" value="1"/>
547 <param name="print_all_reads" value="False" />
548 <conditional name="blast">
549 <param name="blast_output" value="False"/>
550 </conditional>
551 <conditional name="otu">
552 <param name="otu_map" value="False"/>
553 </conditional>
554 </conditional>
555 <param name="e_value" value="1"/>
556 <param name="match" value="2"/>
557 <param name="mismatch" value="-3" />
558 <param name="gap_open" value="5"/>
559 <param name="gap_ext" value="2"/>
560 <param name="ambiguous_letter" value="-3"/>
561 <output name="aligned_forward" file="test6_aligned_forward.fasta" />
562 <output name="aligned_reverse" file="test6_aligned_reverse.fasta" />
563 <output name="unaligned_forward" file="test6_unaligned_forward.fasta" />
564 <output name="unaligned_reverse" file="test6_unaligned_reverse.fasta" />
318 </test> 565 </test>
319 </tests> 566 </tests>
320 <help> 567 <help>
321 <![CDATA[ 568 <![CDATA[
322 **What it does** 569 **What it does**