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comparison pizzly.xml @ 0:f7556cfa4047 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pizzly/ commit a9f602d697c570bc40c6b6ab8e873a11e0eb703d
author iuc
date Wed, 13 Sep 2017 22:40:57 -0400
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1 <tool id="pizzly" name="pizzly" version="0.37.3">
2 <description>- fast fusion detection using kallisto</description>
3 <requirements>
4 <requirement type="package" version="0.37.3">pizzly</requirement>
5 </requirements>
6 <version_command>pizzly --version</version_command>
7 <command detect_errors="exit_code"><![CDATA[
8
9 ## Get reference FASTA
10
11 #if $ref_fa.rfasta.rfasta_source == "history":
12 ln -s '$ref_fa.rfasta.ref_fa_hist' reference.fa &&
13 #else:
14 ln -s '$ref_fa.rfasta.ref_fa_builtin.fields.path' reference.fa &&
15 #end if
16
17
18 ## Get reference GTF
19
20 #if $ref_gtf.rgtf.rgtf_source == "history":
21 ln -s '$ref_gtf.rgtf.ref_gtf_hist' reference.gtf &&
22 #else:
23 ln -s '$ref_gtf.rgtf.ref_gtf_builtin.fields.path' reference.gtf &&
24 #end if
25
26
27 ## Run pizzly
28
29 pizzly
30 --fasta reference.fa
31 --gtf reference.gtf
32 --align-score '$adv.align_score'
33 --insert-size '$adv.insert_size'
34 --k '$adv.kmer_size'
35 $adv.ignore_protein
36 --output out
37 '$kinput.input' &&
38
39
40 ## Convert json output to tabular
41
42 pizzly_flatten_json.py out.json > out.fusions.tab
43
44 ]]></command>
45 <inputs>
46 <section name="kinput" expanded="false" title="Select kallisto fusions file">
47 <param name="input" type="data" format="tabular" label="Output from kallisto quant --fusion" />
48 </section>
49 <section name="ref_fa" expanded="false" title="Select Reference FASTA">
50 <conditional name="rfasta">
51 <param name="rfasta_source" type="select" label="Reference transcriptome FASTA" help="Make sure the FASTA corresponds to the same file used with kallisto quant --fusion">
52 <option value="cached" selected="true">Use a built-in transcriptome</option>
53 <option value="history">Use a FASTA from history</option>
54 </param>
55 <when value="cached">
56 <param name="ref_fa_builtin" type="select" label="Select a built-in FASTA" help="If your transcriptome of interest is not listed, contact your Galaxy administrator">
57 <options from_data_table="all_fasta">
58 <filter type="sort_by" column="2" />
59 <validator type="no_options" message="No FASTA is available for the selected input dataset" />
60 </options>
61 </param>
62 </when>
63 <when value="history">
64 <param name="ref_fa_hist" type="data" format="fasta" label="Select a history FASTA" />
65 </when>
66 </conditional>
67 </section>
68 <section name="ref_gtf" expanded="false" title="Select Reference GTF">
69 <conditional name="rgtf">
70 <param name="rgtf_source" type="select" label="Reference GTF">
71 <option value="cached" selected="true">Use a built-in transcriptome</option>
72 <option value="history">Use a GTF from history</option>
73 </param>
74 <when value="cached">
75 <param name="ref_gtf_builtin" type="select" label="Select a built-in GTF" help="If the GTF file for your transcriptome of interest is not listed, contact your Galaxy administrator">
76 <options from_data_table="all_gtf">
77 <filter type="sort_by" column="2" />
78 <validator type="no_options" message="No GTF file is available." />
79 </options>
80 </param>
81 </when>
82 <when value="history">
83 <param name="ref_gtf_hist" type="data" format="gtf" label="Select a history GTF" />
84 </when>
85 </conditional>
86 </section>
87 <section name="adv" expanded="false" title="Advanced Options">
88 <param name="insert_size" argument="--insert-size" type="integer" value="400" label="Maximum insert size of the paired-end library" help="kallisto will estimate this from the reads, default: 400">
89 <validator type="in_range" min="0" />
90 </param>
91 <param name="align_score" argument="--align-score" type="integer" value="2" label="Number of mismatches allowed" help="default: 2">
92 <validator type="in_range" min="0" />
93 </param>
94 <param name="kmer_size" argument="--k" type="integer" value="31" label="K-mer size used to create the kallisto index" help="default: 31">
95 <validator type="in_range" min="0" />
96 </param>
97 <param name="ignore_protein" argument="--ignore-protein" type="boolean" truevalue="--ignore-protein" falsevalue="" checked="false" label="Ignore protein coding information in annotation" help="Warning: this will probably lead to an increase in the number of false positives reported"/>
98 </section>
99 </inputs>
100 <outputs>
101 <data name="fusions_tab" format="tabular" from_work_dir="out.fusions.tab" label="${tool.name} on ${on_string}: Table"/>
102 <data name="fusions_fa" format="fasta" from_work_dir="out.fusions.fasta" label="${tool.name} on ${on_string}: Fasta"/>
103 </outputs>
104 <tests>
105 <test>
106 <param name="rfasta_source" value="history" />
107 <param name="rgtf_source" value="history" />
108 <param name="input" ftype="tabular" value="fusion.txt" />
109 <param name="ref_fa_hist" ftype="fasta" value="ref.fasta.gz" />
110 <param name="ref_gtf_hist" ftype="gtf" value="ref.gtf.gz" />
111 <output name="fusions_tab" file="out.fusions.tab" ftype="tabular" />
112 <output name="fusions_fa" file="out.fusions.fasta" ftype="fasta" />
113 </test>
114 </tests>
115 <help><![CDATA[
116
117 .. class:: infomark
118
119 **What it does**
120
121 pizzly_ is a program for detecting gene fusions from RNA-Seq data of cancer samples.
122
123 pizzly introduces a novel approach to fusion detection, it builds on the pseudoalignment idea (that simplifies and accelerates transcript quantification) by inspecting paired reads that cannot be pseudoaligned due to conflicting matches. pizzly filters false positives, assembles new transcripts from the fusion reads, and reports candidate fusions.
124
125 With pizzly, fusion detection from RNA-Seq reads can be performed **in a matter of minutes**.
126
127 .. _pizzly: https://github.com/pmelsted/pizzly
128
129 -----
130
131 **Inputs**
132
133 - one or more tabular files from kallisto quant (run with the --fusion parameter on paired-end fastqs)
134 - a FASTA file containing the reference transcriptome. This must be the same fasta that was used to build the kallisto index.
135 - a GTF file describing the transcriptome. Ensembl transcriptomes recommended.
136
137 pizzly has been tested on Ensembl (versions 75+) and Gencode (version 19+) annotations. The latest Ensembl annotations (version 87 GTF, FASTA) are recommended for running with pizzly.
138
139 -----
140
141 **Outputs**
142
143 Two output files are created containing the filtered fusion calls
144
145 - a tabular file
146 - a FASTA file
147
148 -----
149
150 **More Information**
151
152 Fusion junctions are detected by pizzly using a two-stage method. The first stage is implemented in kallisto and detects individual reads or read pairs, whose constituent parts pseudoalign to a reference transcriptome but that in combination fail to pseudoalign. pizzly takes the output of the potential fusion junctions found by kallisto and performs a detailed analysis of the associated reads by aligning them across the putative junctions. Additionally, pizzly is annotation aware, i.e. it uses information about the genomic coordinates and gene identities of each isoform to identify possible false positives arising from repetitive sequences across the genome.
153
154 ]]></help>
155 <citations>
156 <citation type="doi">10.1101/166322</citation>
157 </citations>
158 </tool>