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comparison chira_extract.xml @ 0:0a3107204741 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
author iuc
date Sun, 19 Jan 2020 16:31:03 -0500
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-1:000000000000 0:0a3107204741
1 <tool id="chira_extract" name="ChiRA extract" version="@WRAPPER_VERSION@0">
2 <description>extrat the chimeras</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <command detect_errors="aggressive"><![CDATA[
8 #set $genomic_fasta = ''
9 #if str($annotation.annot_choice) == "yes":
10 #if str($annotation.fasta_source.fasta_source_selector) == 'history':
11 #set $genomic_fasta = '$annotation.fasta_source.fasta'
12 #else
13 #set $genomic_fasta = '$annotation.fasta_source.fasta_id.fields.path'
14 #end if
15 #end if
16 chira_extract.py
17 -l '$loci'
18 #if str($annotation.annot_choice) == "yes":
19 -g '$annotation.gtf'
20 #if $hybridize:
21 -f '$genomic_fasta'
22 #end if
23 #end if
24 -tc '$tpm_cutoff'
25 -sc '$score_cutoff'
26 -co '$chimeric_overlap'
27 #if str($reference.ref_type) == "single":
28 -f1 '$ref_fasta'
29 #else if str($reference.ref_type) == "split":
30 -f1 '$ref_fasta1'
31 -f2 '$ref_fasta2'
32 #end if
33 '$hybridize'
34 -p "\${GALAXY_SLOTS:-2}"
35 -o ./
36 ]]></command>
37
38 <inputs>
39 <param format="tabular" name="loci" type="data" label="File containing CRLs information"/>
40 <conditional name="annotation">
41 <param name="annot_choice" type="select" label="Have genomic information?"
42 help="Selecet Yes if you have an annotation file and provide corresponding genomic fasta file">
43 <option value="yes">Yes</option>
44 <option value="no">No</option>
45 </param>
46 <when value="yes">
47 <param format="gtf,gff" name="gtf" type="data" label="Annotations in GTF format"/>
48 <conditional name="fasta_source">
49 <param name="fasta_source_selector" type="select" label="Choose the source for the FASTA file">
50 <option value="history" selected="true">History</option>
51 <option value="preloaded">Server indexed files</option>
52 </param>
53 <when value="history">
54 <param name="fasta" type="data" format="fasta" label="FASTA file" />
55 </when>
56 <when value="preloaded">
57 <param name="fasta_id" type="select">
58 <options from_data_table="fasta_indexes" />
59 </param>
60 </when>
61 </conditional>
62 </when>
63 <when value="no">
64 <!-- Do nothing -->
65 </when>
66 </conditional>
67 <param name="tpm_cutoff" type="float" value="0" label="TPM cut-off" min="0" max="1"
68 help="Transcripts with less than this percentile TPMs will be discarded in the final output. [0-1.0]"/>
69 <param name="score_cutoff" type="float" value="0" label="Score cut-off" min="0" max="2"
70 help="Hybrids with less than this score will be discarded in the final output. [0-2.0]"/>
71 <param name="chimeric_overlap" type="integer" value="2"
72 label=" Maximum number of bases allowed between the chimericsegments of a read"/>
73 <conditional name="reference">
74 <param name="ref_type" type="select" label="Did you use single or split reference for alignment?">
75 <option value="split">Split reference</option>
76 <option value="single">Single reference</option>
77 </param>
78 <when value="split">
79 <param format="fasta" name="ref_fasta1" type="data" label="Reference FASTA file"
80 help="Reference fasta file"/>
81 <param format="fasta" name="ref_fasta2" type="data" label="Second reference FASTA file"
82 help="Second reference fasta file."/>
83 </when>
84 <when value="single">
85 <param format="fasta" name="ref_fasta" type="data" label="Reference FASTA file"
86 help="Reference fasta file"/>
87 </when>
88 </conditional>
89 <param name="hybridize" type="boolean" truevalue="-r" falsevalue="" checked="false" />
90 </inputs>
91
92 <outputs>
93 <data format="tabular" name="chimeras" from_work_dir="chimeras" label="ChiRA chimeric reads on ${on_string}"/>
94 <data format="tabular" name="singletons" from_work_dir="singletons" label="ChiRA singleton reads on ${on_string}"/>
95 </outputs>
96
97 <tests>
98 <test expect_num_outputs="2">
99 <param name="loci" value="loci.counts"/>
100 <param name="ref_type" value="split"/>
101 <param name="ref_fasta1" value="ref1.fasta"/>
102 <param name="ref_fasta2" value="ref2.fasta"/>
103 <param name="annot_choice" value="no"/>
104 <param name="hybridize" value="true" />
105 <output name="chimeras" file="chimeras" sort="True"/>
106 <output name="singletons" file="singletons" sort="True"/>
107 </test>
108 </tests>
109 <help>
110
111 .. class:: infomark
112
113 **What it does**
114
115 This tool extracts the best chimeric alignments for each read. User can optionally hybridize the loci where the chimeric arms are mapping to.
116
117 **Inputs**
118
119 * Tabular file containing CRLs information
120 * Annotation GTF file
121 * Reference fasta files. Provide both in case of split reference.
122 * If your alignments are merged at genomic level in previous step (chira merge), then provide a reference genomic fasta fille.
123
124 **Output**
125
126 * Tabular file containing chimeras information
127 </help>
128 <expand macro="citations" />
129 </tool>
130