Mercurial > repos > iuc > kallisto_quant

annotate kallisto_quant.xml @ 4:b818b23df1e0 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 011de86c970114d5ae22f76e9ee8e2d86c190063
author iuc
date Sat, 09 Dec 2017 05:33:38 -0500
parents 2754990eb583
children 10c98fab6c5a
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
diff changeset
1 <?xml version="1.0"?>
4
b818b23df1e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 011de86c970114d5ae22f76e9ee8e2d86c190063
iuc
parents: 3
diff changeset
2 <tool id="kallisto_quant" name="Kallisto quant" version="@VERSION@.3">
0
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
diff changeset
3 <description>- quantify abundances of RNA-Seq transcripts</description>
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
diff changeset
4 <macros>
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
diff changeset
5 <import>macros.xml</import>
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
diff changeset
6 </macros>
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
diff changeset
7 <expand macro="requirements" />
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
diff changeset
8 <command detect_errors="exit_code">
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
diff changeset
9 <![CDATA[
4
b818b23df1e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 011de86c970114d5ae22f76e9ee8e2d86c190063
iuc
parents: 3
diff changeset
10 #if $reference_transcriptome.reference_transcriptome_source == "history":
b818b23df1e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 011de86c970114d5ae22f76e9ee8e2d86c190063
iuc
parents: 3
diff changeset
11 ln -s '$reference_transcriptome.reference' reference.fa &&
0
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
diff changeset
12 kallisto index reference.fa -i reference.kallisto &&
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
diff changeset
13 #set index_path = 'reference.kallisto'
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
diff changeset
14 #else:
4
b818b23df1e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 011de86c970114d5ae22f76e9ee8e2d86c190063
iuc
parents: 3
diff changeset
15 #set index_path = $reference_transcriptome.index.fields.path
0
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
diff changeset
16 #end if
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
diff changeset
17 kallisto quant -i '$index_path'
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
diff changeset
18 $bias --bootstrap-samples $bootstrap_samples --seed $seed $fusion $pseudobam
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
diff changeset
19 #if $pseudobam:
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
diff changeset
20 -o .
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
diff changeset
21 #else:
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
diff changeset
22 --threads \${GALAXY_SLOTS:-1}
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
diff changeset
23 -o .
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
diff changeset
24 #end if
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
diff changeset
25 #if str($single_paired.single_paired_selector) == 'single':
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
diff changeset
26 --single
1
7a9158bb6f98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit c695bedd2174ac3a0e2f4c0b1f982a9e047a5302
iuc
parents: 0
diff changeset
27 #set $single_reads = $single_paired.reads
0
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
diff changeset
28 --fragment-length $single_paired.fragment_length
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
diff changeset
29 --sd $single_paired.sd
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
diff changeset
30 '$single_reads'
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
diff changeset
31 #else:
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
diff changeset
32 #if str($single_paired.collection.collection_selector) == 'datasets':
1
7a9158bb6f98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit c695bedd2174ac3a0e2f4c0b1f982a9e047a5302
iuc
parents: 0
diff changeset
33 #set $forward_reads = $single_paired.collection.forward
7a9158bb6f98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit c695bedd2174ac3a0e2f4c0b1f982a9e047a5302
iuc
parents: 0
diff changeset
34 #set $reverse_reads = $single_paired.collection.reverse
0
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
diff changeset
35 #else:
1
7a9158bb6f98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit c695bedd2174ac3a0e2f4c0b1f982a9e047a5302
iuc
parents: 0
diff changeset
36 #set $forward_reads = $single_paired.collection.reads.forward
7a9158bb6f98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit c695bedd2174ac3a0e2f4c0b1f982a9e047a5302
iuc
parents: 0
diff changeset
37 #set $reverse_reads = $single_paired.collection.reads.reverse
0
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
diff changeset
38 #end if
1
7a9158bb6f98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit c695bedd2174ac3a0e2f4c0b1f982a9e047a5302
iuc
parents: 0
diff changeset
39 #set $reads = "'%s' '%s'" % ($forward_reads, $reverse_reads)
7a9158bb6f98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit c695bedd2174ac3a0e2f4c0b1f982a9e047a5302
iuc
parents: 0
diff changeset
40 $reads
0
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
diff changeset
41 #end if
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
diff changeset
42 #if $pseudobam:
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
diff changeset
43 | samtools sort -O bam -@ \${GALAXY_SLOTS:-1} -o '$pseudobam_output' -
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
diff changeset
44 #end if
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
diff changeset
45 && cat run_info.json
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
diff changeset
46 ]]>
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
diff changeset
47 </command>
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
diff changeset
48 <inputs>
4
b818b23df1e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 011de86c970114d5ae22f76e9ee8e2d86c190063
iuc
parents: 3
diff changeset
49 <expand macro="reference_input" />
0
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
diff changeset
50 <conditional name="single_paired">
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
diff changeset
51 <param name="single_paired_selector" type="select" label="Single-end or paired reads">
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
diff changeset
52 <option value="single" selected="true">Single-end</option>
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
diff changeset
53 <option value="paired">Paired</option>
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
diff changeset
54 </param>
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
diff changeset
55 <when value="single">
1
7a9158bb6f98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit c695bedd2174ac3a0e2f4c0b1f982a9e047a5302
iuc
parents: 0
diff changeset
56 <param name="reads" type="data" format="fastq,fastq.gz" label="Reads in FASTQ format" />
0
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
diff changeset
57 <param name="fragment_length" argument="--fragment-length" type="integer" value="200" label="Average fragment length" help="Illumina typically produces reads of 180-200bp" />
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
diff changeset
58 <param argument="--sd" type="integer" value="20" label="Estimated standard deviation of fragment length" />
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
diff changeset
59 </when>
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
diff changeset
60 <when value="paired">
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
diff changeset
61 <conditional name="collection">
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
diff changeset
62 <param name="collection_selector" type="select" label="Collection or individual datasets">
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
diff changeset
63 <option value="datasets" selected="true">Individual files</option>
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
diff changeset
64 <option value="collection">Pair or list of pairs</option>
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
diff changeset
65 </param>
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
diff changeset
66 <when value="datasets">
1
7a9158bb6f98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit c695bedd2174ac3a0e2f4c0b1f982a9e047a5302
iuc
parents: 0
diff changeset
67 <param name="forward" type="data" format="fastq,fastq.gz" label="Forward reads" />
7a9158bb6f98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit c695bedd2174ac3a0e2f4c0b1f982a9e047a5302
iuc
parents: 0
diff changeset
68 <param name="reverse" type="data" format="fastq,fastq.gz" label="Reverse reads" />
0
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
diff changeset
69 </when>
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
diff changeset
70 <when value="collection">
1
7a9158bb6f98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit c695bedd2174ac3a0e2f4c0b1f982a9e047a5302
iuc
parents: 0
diff changeset
71 <param name="reads" type="data_collection" format="fastq,fastq.gz" collection_type="paired" label="Collection of reads" />
0
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
diff changeset
72 </when>
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
diff changeset
73 </conditional>
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
diff changeset
74 </when>
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
diff changeset
75 </conditional>
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
diff changeset
76 <param argument="--bias" type="boolean" truevalue="--bias" falsevalue="" label="Perform sequence based bias correction" />
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
diff changeset
77 <param name="bootstrap_samples" argument="--bootstrap-samples" type="integer" value="0" label="Number of bootstrap samples" help="default: 0" />
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
diff changeset
78 <param argument="--seed" type="integer" value="42" label="Seed for the bootstrap sampling" help="default: 42" />
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
diff changeset
79 <param argument="--fusion" type="boolean" truevalue="--fusion" falsevalue="" label="Search for fusions" help="for Pizzly" />
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
diff changeset
80 <param argument="--pseudobam" type="boolean" truevalue="--pseudobam" falsevalue="" label="Output pseudoalignments in BAM format" />
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
diff changeset
81 </inputs>
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
diff changeset
82 <outputs>
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
diff changeset
83 <data format="h5" name="abundance_h5" from_work_dir="abundance.h5" label="${tool.name} on ${on_string}: Abundances (HDF5)" />
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
diff changeset
84 <data format="tabular" name="abundance_tab" from_work_dir="abundance.tsv" label="${tool.name} on ${on_string}: Abundances (tabular)" />
3
2754990eb583 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit da0d5249fc7bd787ace5dac67bf273891756f324
iuc
parents: 1
diff changeset
85 <data format="bam" name="pseudobam_output" from_work_dir="abundance.txt" label="${tool.name} on ${on_string}: Pseudoalignments">
0
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
diff changeset
86 <filter>pseudobam</filter>
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
diff changeset
87 </data>
3
2754990eb583 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit da0d5249fc7bd787ace5dac67bf273891756f324
iuc
parents: 1
diff changeset
88 <data format="tabular" name="fusion_output" from_work_dir="fusion.txt" label="${tool.name} on ${on_string}: Pizzly input (tabular)">
2754990eb583 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit da0d5249fc7bd787ace5dac67bf273891756f324
iuc
parents: 1
diff changeset
89 <filter>fusion</filter>
2754990eb583 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit da0d5249fc7bd787ace5dac67bf273891756f324
iuc
parents: 1
diff changeset
90 </data>
0
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
diff changeset
91 </outputs>
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
diff changeset
92 <tests>
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
diff changeset
93 <test>
4
b818b23df1e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 011de86c970114d5ae22f76e9ee8e2d86c190063
iuc
parents: 3
diff changeset
94 <param name="reference_transcriptome_source" value="history" />
0
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
diff changeset
95 <param name="reference" ftype="fasta" value="mm10_chrM.fa" />
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
diff changeset
96 <param name="single_paired_selector" value="paired" />
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
diff changeset
97 <param name="collection_selector" value="datasets" />
1
7a9158bb6f98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit c695bedd2174ac3a0e2f4c0b1f982a9e047a5302
iuc
parents: 0
diff changeset
98 <param name="forward" ftype="fastq" value="mm10_chrM-1.f.fq" />
7a9158bb6f98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit c695bedd2174ac3a0e2f4c0b1f982a9e047a5302
iuc
parents: 0
diff changeset
99 <param name="reverse" ftype="fastq" value="mm10_chrM-1.r.fq" />
0
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
diff changeset
100 <output name="abundance_tab" file="kallisto_quant_out1.tab" ftype="tabular" />
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
diff changeset
101 </test>
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
diff changeset
102 <test>
4
b818b23df1e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 011de86c970114d5ae22f76e9ee8e2d86c190063
iuc
parents: 3
diff changeset
103 <param name="reference_transcriptome_source" value="history" />
0
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
diff changeset
104 <param name="reference" ftype="fasta" value="mm10_chrM.fa" />
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
diff changeset
105 <param name="single_paired_selector" value="paired" />
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
diff changeset
106 <param name="collection_selector" value="collection" />
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
diff changeset
107 <param name="reads">
1
7a9158bb6f98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit c695bedd2174ac3a0e2f4c0b1f982a9e047a5302
iuc
parents: 0
diff changeset
108 <collection type="paired">
7a9158bb6f98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit c695bedd2174ac3a0e2f4c0b1f982a9e047a5302
iuc
parents: 0
diff changeset
109 <element name="forward" value="mm10_chrM-1.f.fq" />
7a9158bb6f98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit c695bedd2174ac3a0e2f4c0b1f982a9e047a5302
iuc
parents: 0
diff changeset
110 <element name="reverse" value="mm10_chrM-1.r.fq" />
0
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
diff changeset
111 </collection>
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
diff changeset
112 </param>
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
diff changeset
113 <output name="abundance_tab" file="kallisto_quant_out2.tab" ftype="tabular" />
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
diff changeset
114 </test>
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
diff changeset
115 <test>
4
b818b23df1e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 011de86c970114d5ae22f76e9ee8e2d86c190063
iuc
parents: 3
diff changeset
116 <param name="reference_transcriptome_source" value="history" />
0
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
diff changeset
117 <param name="reference" ftype="fasta" value="mm10_chrM.fa" />
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
diff changeset
118 <param name="single_paired_selector" value="single" />
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
diff changeset
119 <param name="collection_selector" value="collection" />
1
7a9158bb6f98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit c695bedd2174ac3a0e2f4c0b1f982a9e047a5302
iuc
parents: 0
diff changeset
120 <param name="reads" ftype="fastq" value="mm10_chrM-1.f.fq" />
0
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
diff changeset
121 <output name="abundance_tab" file="kallisto_quant_out3.tab" ftype="tabular" />
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
diff changeset
122 </test>
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
diff changeset
123 <test>
4
b818b23df1e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 011de86c970114d5ae22f76e9ee8e2d86c190063
iuc
parents: 3
diff changeset
124 <param name="reference_transcriptome_source" value="history" />
0
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
diff changeset
125 <param name="reference" ftype="fasta" value="felCat8_chrM.fa" />
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
diff changeset
126 <param name="single_paired_selector" value="paired" />
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
diff changeset
127 <param name="collection_selector" value="datasets" />
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
diff changeset
128 <param name="pseudobam" value="true" />
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
diff changeset
129 <param name="forward" ftype="fastq" value="felCat8_chrM_F.fq" />
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
diff changeset
130 <param name="reverse" ftype="fastq" value="felCat8_chrM_R.fq" />
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
diff changeset
131 <output name="abundance_tab" file="kallisto_quant_out4.tab" ftype="tabular" />
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
diff changeset
132 <output name="pseudobam_output" file="kallisto_quant_out4.bam" ftype="bam" />
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
diff changeset
133 </test>
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
diff changeset
134 <test>
4
b818b23df1e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 011de86c970114d5ae22f76e9ee8e2d86c190063
iuc
parents: 3
diff changeset
135 <param name="reference_transcriptome_source" value="cached" />
0
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
diff changeset
136 <param name="single_paired_selector" value="paired" />
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
diff changeset
137 <param name="collection_selector" value="datasets" />
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
diff changeset
138 <param name="pseudobam" value="true" />
1
7a9158bb6f98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit c695bedd2174ac3a0e2f4c0b1f982a9e047a5302
iuc
parents: 0
diff changeset
139 <param name="forward" ftype="fastq" dbkey="sacCer2" value="sacCer2_chrM_F.fq.gz" />
0
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
diff changeset
140 <param name="reverse" ftype="fastq" dbkey="sacCer2" value="sacCer2_chrM_R.fq" />
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
diff changeset
141 <output name="abundance_tab" file="kallisto_quant_out5.tab" ftype="tabular" />
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
diff changeset
142 <output name="pseudobam_output" file="kallisto_quant_out5.bam" ftype="bam" />
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
diff changeset
143 </test>
3
2754990eb583 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit da0d5249fc7bd787ace5dac67bf273891756f324
iuc
parents: 1
diff changeset
144 <test>
4
b818b23df1e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 011de86c970114d5ae22f76e9ee8e2d86c190063
iuc
parents: 3
diff changeset
145 <param name="reference_transcriptome_source" value="history" />
3
2754990eb583 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit da0d5249fc7bd787ace5dac67bf273891756f324
iuc
parents: 1
diff changeset
146 <param name="reference" ftype="fasta" value="hg38_transcripts.fa" />
2754990eb583 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit da0d5249fc7bd787ace5dac67bf273891756f324
iuc
parents: 1
diff changeset
147 <param name="single_paired_selector" value="paired" />
2754990eb583 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit da0d5249fc7bd787ace5dac67bf273891756f324
iuc
parents: 1
diff changeset
148 <param name="collection_selector" value="datasets" />
2754990eb583 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit da0d5249fc7bd787ace5dac67bf273891756f324
iuc
parents: 1
diff changeset
149 <param name="fusion" value="true" />
2754990eb583 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit da0d5249fc7bd787ace5dac67bf273891756f324
iuc
parents: 1
diff changeset
150 <param name="forward" ftype="fastq" dbkey="hg38" value="hg38_F.fq.gz" />
2754990eb583 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit da0d5249fc7bd787ace5dac67bf273891756f324
iuc
parents: 1
diff changeset
151 <param name="reverse" ftype="fastq" dbkey="hg38" value="hg38_R.fq.gz" />
2754990eb583 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit da0d5249fc7bd787ace5dac67bf273891756f324
iuc
parents: 1
diff changeset
152 <output name="fusion_output" file="fusion.txt" ftype="tabular" />
2754990eb583 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit da0d5249fc7bd787ace5dac67bf273891756f324
iuc
parents: 1
diff changeset
153 </test>
2754990eb583 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit da0d5249fc7bd787ace5dac67bf273891756f324
iuc
parents: 1
diff changeset
154
0
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
diff changeset
155 </tests>
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
diff changeset
156 <help>
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
diff changeset
157 <![CDATA[
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
diff changeset
158 kallisto 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. On benchmarks with standard RNA-Seq data, kallisto can quantify 30 million human reads in less than 3 minutes on a Mac desktop computer using only the read sequences and a transcriptome index that itself takes less than 10 minutes to build. Pseudoalignment of reads preserves the key information needed for quantification, and kallisto is therefore not only fast, but also as accurate as existing quantification tools. In fact, because the pseudoalignment procedure is robust to errors in the reads, in many benchmarks kallisto significantly outperforms existing tools.
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
diff changeset
159 ]]>
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
diff changeset
160 </help>
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
diff changeset
161 <expand macro="citations" />
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
parents:
diff changeset
162 </tool>