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comparison kallisto_quant.xml @ 1:7a9158bb6f98 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit c695bedd2174ac3a0e2f4c0b1f982a9e047a5302
author iuc
date Mon, 07 Aug 2017 13:25:33 -0400
parents 59a4c97b85d6
children 2754990eb583
comparison
equal deleted inserted replaced
0:59a4c97b85d6 1:7a9158bb6f98
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="kallisto_quant" name="Kallisto quant" version="@VERSION@.0"> 2 <tool id="kallisto_quant" name="Kallisto quant" version="@VERSION@.1">
3 <description>- quantify abundances of RNA-Seq transcripts</description> 3 <description>- quantify abundances of RNA-Seq transcripts</description>
4 <macros> 4 <macros>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 </macros> 6 </macros>
7 <expand macro="requirements" /> 7 <expand macro="requirements" />
22 --threads \${GALAXY_SLOTS:-1} 22 --threads \${GALAXY_SLOTS:-1}
23 -o . 23 -o .
24 #end if 24 #end if
25 #if str($single_paired.single_paired_selector) == 'single': 25 #if str($single_paired.single_paired_selector) == 'single':
26 --single 26 --single
27 #set $single_reads = "' '".join(str($single_paired.reads).split(',')) 27 #set $single_reads = $single_paired.reads
28 --fragment-length $single_paired.fragment_length 28 --fragment-length $single_paired.fragment_length
29 --sd $single_paired.sd 29 --sd $single_paired.sd
30 '$single_reads' 30 '$single_reads'
31 #else: 31 #else:
32 #if str($single_paired.collection.collection_selector) == 'datasets': 32 #if str($single_paired.collection.collection_selector) == 'datasets':
33 #set $forward_reads = str($single_paired.collection.forward).split(',') 33 #set $forward_reads = $single_paired.collection.forward
34 #set $reverse_reads = str($single_paired.collection.reverse).split(',') 34 #set $reverse_reads = $single_paired.collection.reverse
35 #else: 35 #else:
36 #set $forward_reads = [str($read.forward) for $read in $single_paired.collection.reads] 36 #set $forward_reads = $single_paired.collection.reads.forward
37 #set $reverse_reads = [str($read.reverse) for $read in $single_paired.collection.reads] 37 #set $reverse_reads = $single_paired.collection.reads.reverse
38 #end if 38 #end if
39 #set $tuplexed_reads = zip($forward_reads, $reverse_reads) 39 #set $reads = "'%s' '%s'" % ($forward_reads, $reverse_reads)
40 #set $multiplexed_reads = [] 40 $reads
41 #for read_pair in $tuplexed_reads:
42 ${multiplexed_reads.extend([read for read in read_pair])}
43 #end for
44 #set $reads = "' '".join($multiplexed_reads)
45 '$reads'
46 #end if 41 #end if
47 #if $pseudobam: 42 #if $pseudobam:
48 | samtools sort -O bam -@ \${GALAXY_SLOTS:-1} -o '$pseudobam_output' - 43 | samtools sort -O bam -@ \${GALAXY_SLOTS:-1} -o '$pseudobam_output' -
49 #end if 44 #end if
50 && cat run_info.json 45 && cat run_info.json
72 <param name="single_paired_selector" type="select" label="Single-end or paired reads"> 67 <param name="single_paired_selector" type="select" label="Single-end or paired reads">
73 <option value="single" selected="true">Single-end</option> 68 <option value="single" selected="true">Single-end</option>
74 <option value="paired">Paired</option> 69 <option value="paired">Paired</option>
75 </param> 70 </param>
76 <when value="single"> 71 <when value="single">
77 <param name="reads" type="data" format="fastq" multiple="True" label="Reads in FASTQ format" /> 72 <param name="reads" type="data" format="fastq,fastq.gz" label="Reads in FASTQ format" />
78 <param name="fragment_length" argument="--fragment-length" type="integer" value="200" label="Average fragment length" help="Illumina typically produces reads of 180-200bp" /> 73 <param name="fragment_length" argument="--fragment-length" type="integer" value="200" label="Average fragment length" help="Illumina typically produces reads of 180-200bp" />
79 <param argument="--sd" type="integer" value="20" label="Estimated standard deviation of fragment length" /> 74 <param argument="--sd" type="integer" value="20" label="Estimated standard deviation of fragment length" />
80 </when> 75 </when>
81 <when value="paired"> 76 <when value="paired">
82 <conditional name="collection"> 77 <conditional name="collection">
83 <param name="collection_selector" type="select" label="Collection or individual datasets"> 78 <param name="collection_selector" type="select" label="Collection or individual datasets">
84 <option value="datasets" selected="true">Individual files</option> 79 <option value="datasets" selected="true">Individual files</option>
85 <option value="collection">Pair or list of pairs</option> 80 <option value="collection">Pair or list of pairs</option>
86 </param> 81 </param>
87 <when value="datasets"> 82 <when value="datasets">
88 <param name="forward" type="data" format="fastq" multiple="True" label="Forward reads" /> 83 <param name="forward" type="data" format="fastq,fastq.gz" label="Forward reads" />
89 <param name="reverse" type="data" format="fastq" multiple="True" label="Reverse reads" /> 84 <param name="reverse" type="data" format="fastq,fastq.gz" label="Reverse reads" />
90 </when> 85 </when>
91 <when value="collection"> 86 <when value="collection">
92 <param name="reads" type="data_collection" format="fastq" collection_type="list:paired" label="Collection of reads" /> 87 <param name="reads" type="data_collection" format="fastq,fastq.gz" collection_type="paired" label="Collection of reads" />
93 </when> 88 </when>
94 </conditional> 89 </conditional>
95 </when> 90 </when>
96 </conditional> 91 </conditional>
97 <param argument="--bias" type="boolean" truevalue="--bias" falsevalue="" label="Perform sequence based bias correction" /> 92 <param argument="--bias" type="boolean" truevalue="--bias" falsevalue="" label="Perform sequence based bias correction" />
111 <test> 106 <test>
112 <param name="reference_genome_source" value="history" /> 107 <param name="reference_genome_source" value="history" />
113 <param name="reference" ftype="fasta" value="mm10_chrM.fa" /> 108 <param name="reference" ftype="fasta" value="mm10_chrM.fa" />
114 <param name="single_paired_selector" value="paired" /> 109 <param name="single_paired_selector" value="paired" />
115 <param name="collection_selector" value="datasets" /> 110 <param name="collection_selector" value="datasets" />
116 <param name="forward" ftype="fastq" value="mm10_chrM-1.f.fq,mm10_chrM-2.f.fq,mm10_chrM-3.f.fq,mm10_chrM-4.f.fq,mm10_chrM-5.f.fq" /> 111 <param name="forward" ftype="fastq" value="mm10_chrM-1.f.fq" />
117 <param name="reverse" ftype="fastq" value="mm10_chrM-1.r.fq,mm10_chrM-2.r.fq,mm10_chrM-3.r.fq,mm10_chrM-4.r.fq,mm10_chrM-5.r.fq" /> 112 <param name="reverse" ftype="fastq" value="mm10_chrM-1.r.fq" />
118 <output name="abundance_tab" file="kallisto_quant_out1.tab" ftype="tabular" /> 113 <output name="abundance_tab" file="kallisto_quant_out1.tab" ftype="tabular" />
119 </test> 114 </test>
120 <test> 115 <test>
121 <param name="reference_genome_source" value="history" /> 116 <param name="reference_genome_source" value="history" />
122 <param name="reference" ftype="fasta" value="mm10_chrM.fa" /> 117 <param name="reference" ftype="fasta" value="mm10_chrM.fa" />
123 <param name="single_paired_selector" value="paired" /> 118 <param name="single_paired_selector" value="paired" />
124 <param name="collection_selector" value="collection" /> 119 <param name="collection_selector" value="collection" />
125 <param name="reads"> 120 <param name="reads">
126 <collection type="list:paired"> 121 <collection type="paired">
127 <element name="p1"> 122 <element name="forward" value="mm10_chrM-1.f.fq" />
128 <collection type="paired"> 123 <element name="reverse" value="mm10_chrM-1.r.fq" />
129 <element name="forward" value="mm10_chrM-1.f.fq" />
130 <element name="reverse" value="mm10_chrM-1.r.fq" />
131 </collection>
132 </element>
133 <element name="p2">
134 <collection type="paired">
135 <element name="forward" value="mm10_chrM-2.f.fq" />
136 <element name="reverse" value="mm10_chrM-2.r.fq" />
137 </collection>
138 </element>
139 <element name="p3">
140 <collection type="paired">
141 <element name="forward" value="mm10_chrM-3.f.fq" />
142 <element name="reverse" value="mm10_chrM-3.r.fq" />
143 </collection>
144 </element>
145 <element name="p4">
146 <collection type="paired">
147 <element name="forward" value="mm10_chrM-4.f.fq" />
148 <element name="reverse" value="mm10_chrM-4.r.fq" />
149 </collection>
150 </element>
151 <element name="p5">
152 <collection type="paired">
153 <element name="forward" value="mm10_chrM-5.f.fq" />
154 <element name="reverse" value="mm10_chrM-5.r.fq" />
155 </collection>
156 </element>
157 </collection> 124 </collection>
158 </param> 125 </param>
159 <output name="abundance_tab" file="kallisto_quant_out2.tab" ftype="tabular" /> 126 <output name="abundance_tab" file="kallisto_quant_out2.tab" ftype="tabular" />
160 </test> 127 </test>
161 <test> 128 <test>
162 <param name="reference_genome_source" value="history" /> 129 <param name="reference_genome_source" value="history" />
163 <param name="reference" ftype="fasta" value="mm10_chrM.fa" /> 130 <param name="reference" ftype="fasta" value="mm10_chrM.fa" />
164 <param name="single_paired_selector" value="single" /> 131 <param name="single_paired_selector" value="single" />
165 <param name="collection_selector" value="collection" /> 132 <param name="collection_selector" value="collection" />
166 <param name="reads" ftype="fastq" value="mm10_chrM-1.f.fq,mm10_chrM-2.f.fq,mm10_chrM-3.f.fq,mm10_chrM-4.f.fq,mm10_chrM-5.f.fq" /> 133 <param name="reads" ftype="fastq" value="mm10_chrM-1.f.fq" />
167 <output name="abundance_tab" file="kallisto_quant_out3.tab" ftype="tabular" /> 134 <output name="abundance_tab" file="kallisto_quant_out3.tab" ftype="tabular" />
168 </test> 135 </test>
169 <test> 136 <test>
170 <param name="reference_genome_source" value="history" /> 137 <param name="reference_genome_source" value="history" />
171 <param name="reference" ftype="fasta" value="felCat8_chrM.fa" /> 138 <param name="reference" ftype="fasta" value="felCat8_chrM.fa" />
180 <test> 147 <test>
181 <param name="reference_genome_source" value="cached" /> 148 <param name="reference_genome_source" value="cached" />
182 <param name="single_paired_selector" value="paired" /> 149 <param name="single_paired_selector" value="paired" />
183 <param name="collection_selector" value="datasets" /> 150 <param name="collection_selector" value="datasets" />
184 <param name="pseudobam" value="true" /> 151 <param name="pseudobam" value="true" />
185 <param name="forward" ftype="fastq" dbkey="sacCer2" value="sacCer2_chrM_F.fq" /> 152 <param name="forward" ftype="fastq" dbkey="sacCer2" value="sacCer2_chrM_F.fq.gz" />
186 <param name="reverse" ftype="fastq" dbkey="sacCer2" value="sacCer2_chrM_R.fq" /> 153 <param name="reverse" ftype="fastq" dbkey="sacCer2" value="sacCer2_chrM_R.fq" />
187 <output name="abundance_tab" file="kallisto_quant_out5.tab" ftype="tabular" /> 154 <output name="abundance_tab" file="kallisto_quant_out5.tab" ftype="tabular" />
188 <output name="pseudobam_output" file="kallisto_quant_out5.bam" ftype="bam" /> 155 <output name="pseudobam_output" file="kallisto_quant_out5.bam" ftype="bam" />
189 </test> 156 </test>
190 </tests> 157 </tests>