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comparison sailfish.xml @ 6:5bc9cd008ceb draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sailfish commit 359ddec398e18d3e2a534239b1202691595d1243
author bgruening
date Thu, 13 Apr 2017 08:20:00 -0400
parents 1b4ed566a41c
children
comparison
equal deleted inserted replaced
5:1b4ed566a41c 6:5bc9cd008ceb
1 <tool id="sailfish" name="Sailfish" version="0.10.1"> 1 <tool id="sailfish" name="Sailfish" version="0.10.1.1">
2 <description>transcript quantification from RNA-seq data</description> 2 <description>transcript quantification from RNA-seq data</description>
3 <macros> 3 <macros>
4 <xml name="strandedness"> 4 <xml name="strandedness">
5 <param name="strandedness" type="select" label="Specify the strandedness of the reads"> 5 <param name="strandedness" type="select" label="Specify the strandedness of the reads">
6 <option value="U" selected="True">Not stranded (U)</option> 6 <option value="U" selected="True">Not stranded (U)</option>
8 <option value="SR">read 1 (or single-end read) comes from the reverse strand (SR)</option> 8 <option value="SR">read 1 (or single-end read) comes from the reverse strand (SR)</option>
9 </param> 9 </param>
10 </xml> 10 </xml>
11 </macros> 11 </macros>
12 <requirements> 12 <requirements>
13 <requirement type="package" version="1.0.6">bzip2</requirement>
13 <requirement type="package" version="0.10.1">sailfish</requirement> 14 <requirement type="package" version="0.10.1">sailfish</requirement>
14 </requirements> 15 </requirements>
15 <stdio> 16 <stdio>
16 <exit_code range="1:" /> 17 <exit_code range="1:" />
17 <exit_code range=":-1" /> 18 <exit_code range=":-1" />
31 #set $index_path = './index_dir' 32 #set $index_path = './index_dir'
32 #else: 33 #else:
33 #set $index_path = $refTranscriptSource.index.fields.path 34 #set $index_path = $refTranscriptSource.index.fields.path
34 #end if 35 #end if
35 && 36 &&
37 #set compressed = 'no'
36 #if $single_or_paired.single_or_paired_opts == 'single': 38 #if $single_or_paired.single_or_paired_opts == 'single':
37 #if $single_or_paired.input_singles.ext == 'fasta': 39 #if $single_or_paired.input_singles.ext == 'fasta':
38 #set $ext = 'fasta' 40 #set $ext = 'fasta'
39 #else: 41 #else:
42 #if $single_or_paired.input_singles.is_of_type("fastq.gz"):
43 #set compressed = 'GZ'
44 #else if $single_or_paired.input_singles.is_of_type("fastq.bz2"):
45 #set compressed = 'BZ2'
46 #end if
40 #set $ext = 'fastq' 47 #set $ext = 'fastq'
41 #end if 48 #end if
42 ln -s $single_or_paired.input_singles ./single.$ext && 49 ln -s $single_or_paired.input_singles ./single.$ext &&
43 #else: 50 #else:
44 #if $single_or_paired.input_mate1.ext == 'fasta': 51 #if $single_or_paired.input_mate1.ext == 'fasta':
45 #set $ext = 'fasta' 52 #set $ext = 'fasta'
46 #else: 53 #else:
54 #if $single_or_paired.input_mate1.is_of_type("fastq.gz"):
55 #set compressed = 'GZ'
56 #else if $single_or_paired.input_mate1.is_of_type("fastq.bz2"):
57 #set compressed = 'BZ2'
58 #end if
47 #set $ext = 'fastq' 59 #set $ext = 'fastq'
48 #end if 60 #end if
49 ln -s $single_or_paired.input_mate1 ./mate1.$ext && 61 ln -s $single_or_paired.input_mate1 ./mate1.$ext &&
50 ln -s $single_or_paired.input_mate2 ./mate2.$ext && 62 ln -s $single_or_paired.input_mate2 ./mate2.$ext &&
51 #end if 63 #end if
54 #end if 66 #end if
55 sailfish quant 67 sailfish quant
56 --index $index_path 68 --index $index_path
57 #if $single_or_paired.single_or_paired_opts == 'single': 69 #if $single_or_paired.single_or_paired_opts == 'single':
58 --libType ${single_or_paired.strandedness} 70 --libType ${single_or_paired.strandedness}
59 --unmatedReads ./single.$ext 71 #if $compressed == 'GZ':
72 --unmatedReads <(zcat ./single.$ext)
73 #else if $compressed == 'BZ2':
74 --unmatedReads <(bzcat ./single.$ext)
75 #else:
76 --unmatedReads ./single.$ext
77 #end if
60 #else: 78 #else:
61 --mates1 ./mate1.$ext 79 #if $compressed == 'GZ':
62 --mates2 ./mate2.$ext 80 --mates1 <(zcat ./mate1.$ext)
81 --mates2 <(zcat ./mate2.$ext)
82 #else if $compressed == 'BZ2':
83 --mates1 <(bzcat ./mate1.$ext)
84 --mates2 <(bzcat ./mate2.$ext)
85 #else:
86 --mates1 ./mate1.$ext
87 --mates2 ./mate2.$ext
88 #end if
63 --libType "${single_or_paired.orientation}${single_or_paired.strandedness}" 89 --libType "${single_or_paired.orientation}${single_or_paired.strandedness}"
64 #end if 90 #end if
65 --output ./results 91 --output ./results
66 $biasCorrect 92 $biasCorrect
67 $gcBiasCorrect 93 $gcBiasCorrect
136 <param name="single_or_paired_opts" type="select" label="Is this library mate-paired?"> 162 <param name="single_or_paired_opts" type="select" label="Is this library mate-paired?">
137 <option value="single">Single-end</option> 163 <option value="single">Single-end</option>
138 <option value="paired">Paired-end</option> 164 <option value="paired">Paired-end</option>
139 </param> 165 </param>
140 <when value="single"> 166 <when value="single">
141 <param name="input_singles" type="data" format="fastq,fasta" label="FASTQ/FASTA file" help="FASTQ file." /> 167 <param name="input_singles" type="data" format="fastq,fasta,fastq.gz" label="FASTQ/FASTA file" help="FASTQ file." />
142 <expand macro="strandedness" /> 168 <expand macro="strandedness" />
143 </when> 169 </when>
144 <when value="paired"> 170 <when value="paired">
145 <param name="input_mate1" type="data" format="fastq,fasta" label="Mate pair 1" help="FASTQ file." /> 171 <param name="input_mate1" type="data" format="fastq,fasta,fastq.gz" label="Mate pair 1" help="FASTQ file." />
146 <param name="input_mate2" type="data" format="fastq,fasta" label="Mate pair 2" help="FASTQ file." /> 172 <param name="input_mate2" type="data" format="fastq,fasta,fastq.gz" label="Mate pair 2" help="FASTQ file." />
147 <param name="orientation" type="select" label="Relative orientation of reads within a pair"> 173 <param name="orientation" type="select" label="Relative orientation of reads within a pair">
148 <option value="M">Mates are oriented in the same direction (M = matching)</option> 174 <option value="M">Mates are oriented in the same direction (M = matching)</option>
149 <option value="O">Mates are oriented away from each other (O = outward)</option> 175 <option value="O">Mates are oriented away from each other (O = outward)</option>
150 <option value="I" selected="True">Mates are oriented toward each other (I = inward)</option> 176 <option value="I" selected="True">Mates are oriented toward each other (I = inward)</option>
151 </param> 177 </param>
271 <param name="biasCorrect" value="False" /> 297 <param name="biasCorrect" value="False" />
272 <param name="TranscriptSource" value="history" /> 298 <param name="TranscriptSource" value="history" />
273 <param name="ownFile" value="transcripts.fasta" ftype="fasta" /> 299 <param name="ownFile" value="transcripts.fasta" ftype="fasta" />
274 <output file="sailfish_quant_result1.tab" ftype="tabular" name="output_quant" /> 300 <output file="sailfish_quant_result1.tab" ftype="tabular" name="output_quant" />
275 </test> 301 </test>
302 <test> <!-- gzipped version of above -->
303 <param name="single_or_paired_opts" value="paired" />
304 <param name="input_mate1" value="reads_1.fastq.gz" ftype="fastqsanger.gz" />
305 <param name="input_mate2" value="reads_2.fastq.gz" ftype="fastqsanger.gz" />
306 <param name="biasCorrect" value="False" />
307 <param name="TranscriptSource" value="history" />
308 <param name="ownFile" value="transcripts.fasta" ftype="fasta" />
309 <output file="sailfish_quant_result1.tab" ftype="tabular" name="output_quant" />
310 </test>
276 <test> 311 <test>
277 <param name="single_or_paired_opts" value="paired" /> 312 <param name="single_or_paired_opts" value="paired" />
278 <param name="input_mate1" value="reads_1.fastq" /> 313 <param name="input_mate1" value="reads_1.fastq" />
279 <param name="input_mate2" value="reads_2.fastq" /> 314 <param name="input_mate2" value="reads_2.fastq" />
280 <param name="biasCorrect" value="True" /> 315 <param name="biasCorrect" value="True" />