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comparison kallisto_pseudo.xml @ 0:2953303df011 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
author iuc
date Tue, 22 Aug 2017 04:16:08 -0400
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children 1c75aa5de15e
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-1:000000000000 0:2953303df011
1 <?xml version="1.0"?>
2 <tool id="kallisto_pseudo" name="Kallisto pseudo" version="@VERSION@.0">
3 <description>- run pseudoalignment on RNA-Seq transcripts</description>
4 <macros>
5 <import>macros.xml</import>
6 </macros>
7 <expand macro="requirements" />
8 <command detect_errors="exit_code">
9 <![CDATA[
10 #if $reference_genome.reference_genome_source == "history":
11 ln -s '$reference_genome.reference' reference.fa &&
12 kallisto index reference.fa -i reference.kallisto &&
13 #set index_path = 'reference.kallisto'
14 #else:
15 #set index_path = $reference_genome.index.fields.path
16 #end if
17 kallisto pseudo -i '$index_path'
18 #if $pseudobam:
19 $pseudobam -o .
20 #else:
21 --threads \${GALAXY_SLOTS:-1}
22 -o .
23 #end if
24
25
26 #if str($single_paired.single_paired_selector) == 'single':
27 --single --fragment-length $single_paired.fragment_length
28 --sd $single_paired.sd '$single_paired.reads'
29 #else:
30 #if str($single_paired.collection.collection_selector) == 'collection':
31 '$single_paired.collection.reads.forward'
32 '$single_paired.collection.reads.reverse'
33 #else:
34 #if str($single_paired.collection.fastq_umi.umi) == 'yes':
35 --batch '$batch' --umi
36 #else:
37 '$single_paired.collection.fastq_umi.forward'
38 '$single_paired.collection.fastq_umi.reverse'
39 #end if
40 #end if
41 #end if
42 #if $pseudobam:
43 | samtools sort -O bam -@ \${GALAXY_SLOTS:-1} -o '$pseudobam_output' -
44 #end if
45 && if [ -f run_info.json ] ; then cat run_info.json ; fi &&
46 mkdir outputs &&
47 if [ -f matrix.ec ] ; then mv matrix.ec outputs/Matrix.ec ; fi &&
48 if [ -f matrix.tsv ] ; then mv matrix.tsv outputs/Matrix.tabular ; fi &&
49 if [ -f matrix.cells ] ; then mv matrix.cells outputs/Matrix.cells ; fi &&
50 if [ -f pseudoalignments.tsv ] ; then mv pseudoalignments.tsv outputs/Pseudoalignments.tabular ; fi &&
51 if [ -f pseudoalignments.ec ] ; then mv pseudoalignments.ec outputs/Pseudoalignments.ec ; fi
52 ]]>
53 </command>
54 <configfiles>
55 <configfile name="batch">
56 <![CDATA[
57 #if str($single_paired.single_paired_selector) == 'single':
58 cell1 $single_paired.reads
59 #else:
60 #if str($single_paired.collection.collection_selector) == 'collection':
61 cell1 $single_paired.collection.reads.forward $single_paired.collection.reads.reverse
62 #else:
63 cell1 $single_paired.collection.fastq_umi.forward $single_paired.collection.fastq_umi.reverse
64 #end if
65 #end if
66 ]]>
67 </configfile>
68 </configfiles>
69 <inputs>
70 <conditional name="reference_genome">
71 <param name="reference_genome_source" type="select" label="Reference genome for pseudoalignment">
72 <option value="indexed" selected="true">Use a built-in genome</option>
73 <option value="history">Use a genome from history</option>
74 </param>
75 <when value="indexed">
76 <param name="index" type="select" label="Select a reference genome" help="If your genome of interest is not listed, contact your Galaxy administrator">
77 <options from_data_table="kallisto_indexes">
78 <filter type="sort_by" column="2" />
79 <validator type="no_options" message="No genomes are available for the selected input dataset" />
80 </options>
81 </param>
82 </when>
83 <when value="history">
84 <param name="reference" type="data" format="fasta" label="FASTA reference genome" />
85 </when>
86 </conditional>
87 <conditional name="single_paired">
88 <param name="single_paired_selector" type="select" label="Single-end or paired reads">
89 <option value="single" selected="true">Single-end</option>
90 <option value="paired">Paired</option>
91 </param>
92 <when value="single">
93 <param name="reads" type="data" format="fastq" multiple="True" label="Reads in FASTQ format" />
94 <param name="fragment_length" argument="--fragment-length" type="integer" value="200" label="Average fragment length" />
95 <param argument="--sd" type="integer" value="20" label="Estimated standard deviation of fragment length" />
96 </when>
97 <when value="paired">
98 <conditional name="collection">
99 <param name="collection_selector" type="select" label="Collection or individual datasets">
100 <option value="datasets" selected="true">Individual files</option>
101 <option value="collection">Pair or list of pairs</option>
102 </param>
103 <when value="datasets">
104 <conditional name="fastq_umi">
105 <param name="umi" type="select" label="Pseudoalignment uses UMIs">
106 <option value="no" selected="true">Paired FASTQ</option>
107 <option value="yes">UMI</option>
108 </param>
109 <when value="yes">
110 <param name="forward" type="data" format="tabular" multiple="True" label="UMI file" />
111 <param name="reverse" type="data" format="fastq" multiple="True" label="FASTQ reads" />
112 </when>
113 <when value="no">
114 <param name="forward" type="data" format="fastq" multiple="True" label="Forward reads" />
115 <param name="reverse" type="data" format="fastq" multiple="True" label="Reverse reads" />
116 </when>
117 </conditional>
118 </when>
119 <when value="collection">
120 <param name="reads" type="data_collection" format="fastq" collection_type="paired" label="Collection of reads" />
121 </when>
122 </conditional>
123 </when>
124 </conditional>
125 <param argument="--pseudobam" type="boolean" truevalue="--pseudobam" falsevalue="" label="Output pseudoalignments in BAM format" />
126 </inputs>
127 <outputs>
128 <data format="tabular" name="sample">
129 <discover_datasets pattern="(?P&lt;designation&gt;.+)" directory="outputs" ext="tabular" visible="true" />
130 </data>
131 <data format="bam" name="pseudobam_output" label="${tool.name} on ${on_string}: Pseudoalignments (BAM)">
132 <filter>pseudobam</filter>
133 </data>
134 </outputs>
135 <tests>
136 <test>
137 <param name="reference_genome_source" value="history" />
138 <param name="reference" ftype="fasta" value="mm10_chrM.fa" />
139 <param name="single_paired_selector" value="paired" />
140 <param name="collection_selector" value="datasets" />
141 <param name="umi" value="yes" />
142 <param name="forward" ftype="tabular" value="mm10_chrM.umi" />
143 <param name="reverse" ftype="fastq" value="mm10_chrM-1.r.fq" />
144 <output name="sample">
145 <discovered_dataset designation="Matrix.tabular" file="kallisto_pseudo_out1.tab" ftype="tabular" />
146 <discovered_dataset designation="Matrix.ec" file="kallisto_pseudo_out1.ec" ftype="tabular" />
147 <discovered_dataset designation="Matrix.cells" file="kallisto_pseudo_out1.cells" ftype="tabular" />
148 </output>
149 </test>
150 <test>
151 <param name="reference_genome_source" value="history" />
152 <param name="reference" ftype="fasta" value="mm10_chrM.fa" />
153 <param name="single_paired_selector" value="paired" />
154 <param name="collection_selector" value="collection" />
155 <param name="umi" value="no" />
156 <param name="reads">
157 <collection type="paired">
158 <element name="forward" value="mm10_chrM-1.f.fq" />
159 <element name="reverse" value="mm10_chrM-1.r.fq" />
160 </collection>
161 </param>
162 <output name="sample">
163 <discovered_dataset designation="Pseudoalignments.tabular" file="kallisto_pseudo_out2.tab" ftype="tabular" />
164 <discovered_dataset designation="Pseudoalignments.ec" file="kallisto_pseudo_out2.ec" ftype="tabular" />
165 </output>
166 </test>
167 <test>
168 <param name="reference_genome_source" value="history" />
169 <param name="reference" ftype="fasta" value="mm10_chrM.fa" />
170 <param name="single_paired_selector" value="single" />
171 <param name="collection_selector" value="collection" />
172 <param name="reads" ftype="fastq" value="mm10_chrM-1.f.fq" />
173 <output name="sample">
174 <discovered_dataset designation="Pseudoalignments.tabular" file="kallisto_pseudo_out3.tab" ftype="tabular" />
175 <discovered_dataset designation="Pseudoalignments.ec" file="kallisto_pseudo_out3.ec" ftype="tabular" />
176 </output>
177 </test>
178 <test>
179 <param name="reference_genome_source" value="history" />
180 <param name="reference" ftype="fasta" value="felCat8_chrM.fa" />
181 <param name="single_paired_selector" value="paired" />
182 <param name="collection_selector" value="datasets" />
183 <param name="umi" value="no" />
184 <param name="forward" ftype="fastq" value="felCat8_chrM_F.fq" />
185 <param name="reverse" ftype="fastq" value="felCat8_chrM_R.fq" />
186 <output name="sample">
187 <discovered_dataset designation="Pseudoalignments.tabular" file="kallisto_pseudo_out4.tab" ftype="tabular" />
188 <discovered_dataset designation="Pseudoalignments.ec" file="kallisto_pseudo_out4.ec" ftype="tabular" />
189 </output>
190 </test>
191 <test>
192 <param name="reference_genome_source" value="cached" />
193 <param name="single_paired_selector" value="paired" />
194 <param name="collection_selector" value="datasets" />
195 <param name="pseudobam" value="true" />
196 <param name="forward" ftype="fastq" dbkey="sacCer2" value="sacCer2_chrM_F.fq.gz" />
197 <param name="reverse" ftype="fastq" dbkey="sacCer2" value="sacCer2_chrM_R.fq.gz" />
198 <output name="sample">
199 <discovered_dataset designation="Pseudoalignments.tabular" file="kallisto_pseudo_out5.tab" ftype="tabular" />
200 <discovered_dataset designation="Pseudoalignments.ec" file="kallisto_pseudo_out5.ec" ftype="tabular" />
201 </output>
202 <output name="pseudobam_output" file="kallisto_pseudo_out5.bam" ftype="bam" />
203 </test>
204 <test>
205 <param name="reference_genome_source" value="cached" />
206 <param name="single_paired_selector" value="paired" />
207 <param name="collection_selector" value="datasets" />
208 <param name="umi" value="yes" />
209 <param name="forward" ftype="fastq" dbkey="sacCer2" value="sacCer2_chrM.umi" />
210 <param name="reverse" ftype="fastq" dbkey="sacCer2" value="sacCer2_chrM_R.fq.gz" />
211 <output name="sample">
212 <discovered_dataset designation="Matrix.tabular" file="kallisto_pseudo_out6.tab" ftype="tabular" />
213 <discovered_dataset designation="Matrix.ec" file="kallisto_pseudo_out6.ec" ftype="tabular" />
214 <discovered_dataset designation="Matrix.cells" file="kallisto_pseudo_out6.cells" ftype="tabular" />
215 </output>
216 </test>
217 </tests>
218 <help>
219 <![CDATA[
220 `kallisto <https://pachterlab.github.io/kallisto/manual>`__ is a program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. It is based on the novel idea of pseudoalignment for rapidly determining the compatibility of reads with targets, without the need for alignment.
221 ]]>
222 </help>
223 <expand macro="citations" />
224 </tool>