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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pizzly/ commit 0ad49d906b38e290b860310e73b1f8585ac65d09
author iuc
date Tue, 03 Oct 2017 18:04:46 -0400
parents f7556cfa4047
children
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0:f7556cfa4047 1:91ef4a171202
1 <tool id="pizzly" name="pizzly" version="0.37.3"> 1 <tool id="pizzly" name="pizzly" version="0.37.3.1">
2 <description>- fast fusion detection using kallisto</description> 2 <description>- fast fusion detection using kallisto</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="0.37.3">pizzly</requirement> 4 <requirement type="package" version="0.37.3">pizzly</requirement>
5 </requirements> 5 </requirements>
6 <version_command>pizzly --version</version_command> 6 <version_command>pizzly --version</version_command>
7 <command detect_errors="exit_code"><![CDATA[ 7 <command detect_errors="exit_code"><![CDATA[
8
9 ## Get reference FASTA
10 8
11 #if $ref_fa.rfasta.rfasta_source == "history": 9 ## Get reference FASTA
12 ln -s '$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 10
17 11 #if $ref_fa.rfasta.rfasta_source == "history":
18 ## Get reference GTF 12 ln -s '$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
19 16
20 #if $ref_gtf.rgtf.rgtf_source == "history":
21 ln -s '$ref_gtf.rgtf.ref_gtf_hist' reference.gtf &&
22 #else:
23 ln -s '$ref_gtf.rgtf.ref_gtf_builtin.fields.path' reference.gtf &&
24 #end if
25 17
26 18 ## Get reference GTF
27 ## Run pizzly
28
29 pizzly
30 --fasta reference.fa
31 --gtf reference.gtf
32 --align-score '$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 19
39 20 #if $ref_gtf.rgtf.rgtf_source == "history":
40 ## Convert json output to tabular 21 ln -s '$ref_gtf.rgtf.ref_gtf_hist' reference.gtf &&
22 #else:
23 ln -s '$ref_gtf.rgtf.ref_gtf_builtin.fields.path' reference.gtf &&
24 #end if
41 25
42 pizzly_flatten_json.py out.json > out.fusions.tab 26
27 ## Run pizzly
28
29 pizzly
30 --fasta reference.fa
31 --gtf reference.gtf
32 --align-score '$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 43
44 ]]></command> 44 ]]></command>
45 <inputs> 45 <inputs>
46 <section name="kinput" expanded="false" title="Select kallisto fusions file"> 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" /> 47 <param name="input" type="data" format="tabular" label="Output from kallisto quant --fusion" />
48 </section> 48 </section>
49 <section name="ref_fa" expanded="false" title="Select Reference FASTA"> 49 <section name="ref_fa" expanded="false" title="Select Reference FASTA">
50 <conditional name="rfasta"> 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"> 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> 52 <option value="cached" selected="true">Use a built-in transcriptome</option>
53 <option value="history">Use a FASTA from history</option> 53 <option value="history">Use a FASTA from history</option>
54 </param> 54 </param>
71 <option value="cached" selected="true">Use a built-in transcriptome</option> 71 <option value="cached" selected="true">Use a built-in transcriptome</option>
72 <option value="history">Use a GTF from history</option> 72 <option value="history">Use a GTF from history</option>
73 </param> 73 </param>
74 <when value="cached"> 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"> 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"> 76 <options from_data_table="gene_sets">
77 <filter type="sort_by" column="2" /> 77 <filter type="sort_by" column="2" />
78 <validator type="no_options" message="No GTF file is available." /> 78 <validator type="no_options" message="No GTF file is available." />
79 </options> 79 </options>
80 </param> 80 </param>
81 </when> 81 </when>
82 <when value="history"> 82 <when value="history">
83 <param name="ref_gtf_hist" type="data" format="gtf" label="Select a history GTF" /> 83 <param name="ref_gtf_hist" type="data" format="gtf" label="Select a history GTF" />
84 </when> 84 </when>
85 </conditional> 85 </conditional>
86 </section> 86 </section>
87 <section name="adv" expanded="false" title="Advanced Options"> 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"> 88 <param name="insert_size" argument="--insert-size" type="integer" value="400" min="0" 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" /> 89 <param name="align_score" argument="--align-score" type="integer" value="2" min="0" label="Number of mismatches allowed" help="default: 2" />
90 </param> 90 <param name="kmer_size" argument="--k" type="integer" value="31" min="0" label="K-mer size used to create the kallisto index" help="default: 31" />
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"/> 91 <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> 92 </section>
99 </inputs> 93 </inputs>
100 <outputs> 94 <outputs>
101 <data name="fusions_tab" format="tabular" from_work_dir="out.fusions.tab" label="${tool.name} on ${on_string}: Table"/> 95 <data name="fusions_tab" format="tabular" from_work_dir="out.fusions.tab" label="${tool.name} on ${on_string}: Table"/>
102 <data name="fusions_fa" format="fasta" from_work_dir="out.fusions.fasta" label="${tool.name} on ${on_string}: Fasta"/> 96 <data name="fusions_fa" format="fasta" from_work_dir="out.fusions.fasta" label="${tool.name} on ${on_string}: Fasta"/>
103 </outputs> 97 </outputs>
104 <tests> 98 <tests>
105 <test> 99 <test><!-- Ensure history fasta and gtf work -->
106 <param name="rfasta_source" value="history" /> 100 <param name="rfasta_source" value="history" />
107 <param name="rgtf_source" value="history" /> 101 <param name="rgtf_source" value="history" />
108 <param name="input" ftype="tabular" value="fusion.txt" /> 102 <param name="input" ftype="tabular" value="fusion.txt" />
109 <param name="ref_fa_hist" ftype="fasta" value="ref.fasta.gz" /> 103 <param name="ref_fa_hist" ftype="fasta" value="ref.trans.fasta.gz" />
110 <param name="ref_gtf_hist" ftype="gtf" value="ref.gtf.gz" /> 104 <param name="ref_gtf_hist" ftype="gtf" value="ref.gtf.gz" />
105 <output name="fusions_tab" file="out.fusions.tab" ftype="tabular" />
106 <output name="fusions_fa" file="out.fusions.fasta" ftype="fasta" />
107 </test>
108 <test><!-- Ensure built-in fasta and gtf work -->
109 <param name="rfasta_source" value="cached" />
110 <param name="rgtf_source" value="cached" />
111 <param name="input" ftype="tabular" dbkey="hg38" value="fusion.txt" />
111 <output name="fusions_tab" file="out.fusions.tab" ftype="tabular" /> 112 <output name="fusions_tab" file="out.fusions.tab" ftype="tabular" />
112 <output name="fusions_fa" file="out.fusions.fasta" ftype="fasta" /> 113 <output name="fusions_fa" file="out.fusions.fasta" ftype="fasta" />
113 </test> 114 </test>
114 </tests> 115 </tests>
115 <help><![CDATA[ 116 <help><![CDATA[
116 117
117 .. class:: infomark 118 .. class:: infomark
118 119
119 **What it does** 120 **What it does**
120 121
121 pizzly_ is a program for detecting gene fusions from RNA-Seq data of cancer samples. 122 pizzly_ is a program for detecting gene fusions from RNA-Seq data of cancer samples.
122 123
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 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
125 With pizzly, fusion detection from RNA-Seq reads can be performed **in a matter of minutes**. 126 With pizzly, fusion detection from RNA-Seq reads can be performed **in a matter of minutes**.
126 127
127 .. _pizzly: https://github.com/pmelsted/pizzly 128 .. _pizzly: https://github.com/pmelsted/pizzly
128 129
140 141
141 **Outputs** 142 **Outputs**
142 143
143 Two output files are created containing the filtered fusion calls 144 Two output files are created containing the filtered fusion calls
144 145
145 - a tabular file 146 - a tabular file
146 - a FASTA file 147 - a FASTA file
147 148
148 ----- 149 -----
149 150
150 **More Information** 151 **More Information**
151 152