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comparison chira_extract.xml @ 19:73d2b7a8d94b draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit 8064fa653fe73c9432c76783d6c635d86548d538"
author iuc
date Sun, 19 Dec 2021 15:47:37 +0000
parents e7ee3aadf1a5
children
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18:e7ee3aadf1a5 19:73d2b7a8d94b
1 <tool id="chira_extract" name="ChiRA extract" version="@WRAPPER_VERSION@0"> 1 <tool id="chira_extract" name="ChiRA extract" version="@TOOL_VERSION@1">
2 <description>extrat the chimeras</description> 2 <description>extrat the chimeras</description>
3 <expand macro="bio_tools"/>
4 <macros> 3 <macros>
5 <import>macros.xml</import> 4 <import>macros.xml</import>
6 </macros> 5 </macros>
6 <expand macro="bio_tools"/>
7 <expand macro="requirements" /> 7 <expand macro="requirements" />
8 <command detect_errors="aggressive"><![CDATA[ 8 <command detect_errors="aggressive"><![CDATA[
9 #set $genomic_fasta = '' 9 #set $genomic_fasta = ''
10 #if str($annotation.annot_choice) == "yes": 10 #if str($annotation.annot_choice) == "yes":
11 #if str($annotation.fasta_source.fasta_source_selector) == 'history': 11 #if str($annotation.fasta_source.fasta_source_selector) == 'history':
15 #else 15 #else
16 #set $genomic_fasta = $annotation.fasta_source.fasta_id.fields.path 16 #set $genomic_fasta = $annotation.fasta_source.fasta_id.fields.path
17 #end if 17 #end if
18 #end if 18 #end if
19 chira_extract.py 19 chira_extract.py
20 -l '$loci' 20 --loci '$loci'
21 #if str($annotation.annot_choice) == "yes": 21 #if str($annotation.annot_choice) == "yes":
22 -g '$annotation.gtf' 22 --gtf '$annotation.gtf'
23 #if $hybridize: 23 #if $hybridize:
24 -f '$genomic_fasta' 24 --ref '$genomic_fasta'
25 #end if 25 #end if
26 #end if 26 #end if
27 -tc '$tpm_cutoff' 27 --tpm_cutoff '$tpm_cutoff'
28 -sc '$score_cutoff' 28 --score_cutoff '$score_cutoff'
29 -co '$chimeric_overlap' 29 --chimeric_overlap '$chimeric_overlap'
30 #if str($reference.ref_type) == "single": 30 #if str($reference.ref_type) == "single":
31 -f1 '$reference.ref_fasta' 31 -f1 '$reference.ref_fasta'
32 #else if str($reference.ref_type) == "split": 32 #else if str($reference.ref_type) == "split":
33 -f1 '$reference.ref_fasta1' 33 -f1 '$reference.ref_fasta1'
34 -f2 '$reference.ref_fasta2' 34 -f2 '$reference.ref_fasta2'
35 #end if 35 #end if
36 $hybridize 36 $hybridize
37 $seed_interaction 37 $seed_interaction
38 -sbp '$seed_bp' 38 --seed_bp '$seed_bp'
39 -smpu '$seed_min_pu' 39 --seed_min_pu '$seed_min_pu'
40 -acc '$accessibility' 40 --accessibility '$accessibility'
41 -accw '$acc_width' 41 --acc_width '$acc_width'
42 -m '$intarna_mode' 42 --intarna_mode '$intarna_mode'
43 --temperature $temperature
43 $summarize 44 $summarize
44 -p "\${GALAXY_SLOTS:-2}" 45 --processes "\${GALAXY_SLOTS:-2}"
45 -o ./ 46 --out ./
46 ]]></command> 47 ]]></command>
47 48
48 <inputs> 49 <inputs>
49 <param format="tabular" name="loci" type="data" label="File containing CRLs information"/> 50 <param format="tabular" argument="--loci" type="data" label="File containing CRLs information"/>
50 <conditional name="annotation"> 51 <conditional name="annotation">
51 <param name="annot_choice" type="select" label="Have genomic information?" 52 <param name="annot_choice" type="select" label="Have genomic information?"
52 help="Selecet Yes if you have an annotation file and provide corresponding genomic fasta file"> 53 help="Selecet Yes if you have an annotation file and provide corresponding genomic fasta file">
53 <option value="yes">Yes</option> 54 <option value="yes">Yes</option>
54 <option value="no">No</option> 55 <option value="no">No</option>
55 </param> 56 </param>
56 <when value="yes"> 57 <when value="yes">
57 <param format="gtf,gff" name="gtf" type="data" label="Annotations in GTF format"/> 58 <param format="gtf,gff" argument="--gtf" type="data" label="Annotations in GTF format"/>
58 <conditional name="fasta_source"> 59 <conditional name="fasta_source">
59 <param name="fasta_source_selector" type="select" label="Choose the source for the FASTA file"> 60 <param name="fasta_source_selector" type="select" label="Choose the source for the FASTA file">
60 <option value="history" selected="true">History</option> 61 <option value="history" selected="true">History</option>
61 <option value="preloaded">Server indexed files</option> 62 <option value="preloaded">Server indexed files</option>
62 </param> 63 </param>
63 <when value="history"> 64 <when value="history">
64 <param name="fasta" type="data" format="fasta" label="Genomic FASTA file" /> 65 <param argument="--ref" name="fasta" type="data" format="fasta" label="Genomic FASTA file" />
65 </when> 66 </when>
66 <when value="preloaded"> 67 <when value="preloaded">
67 <param name="fasta_id" type="select" label="Select FASTA index"> 68 <param argument="--ref" name="fasta_id" type="select" label="Select FASTA index">
68 <options from_data_table="fasta_indexes" /> 69 <options from_data_table="fasta_indexes" />
69 </param> 70 </param>
70 </when> 71 </when>
71 </conditional> 72 </conditional>
72 </when> 73 </when>
73 <when value="no"> 74 <when value="no">
74 <!-- Do nothing --> 75 <!-- Do nothing -->
75 </when> 76 </when>
76 </conditional> 77 </conditional>
77 <param name="tpm_cutoff" type="float" value="0" label="TPM cut-off" min="0" max="1" 78 <param argument="--tpm_cutoff" type="float" value="0" label="TPM cut-off" min="0" max="1"
78 help="Transcripts with less than this percentile TPMs will be discarded in the final output. [0-1.0]"/> 79 help="Transcripts with less than this percentile TPMs will be discarded in the final output. [0-1.0]"/>
79 <param name="score_cutoff" type="float" value="0" label="Score cut-off" min="0" max="2" 80 <param argument="--score_cutoff" type="float" value="0" label="Score cut-off" min="0" max="2"
80 help="Hybrids with less than this score will be discarded in the final output. [0-2.0]"/> 81 help="Hybrids with less than this score will be discarded in the final output. [0-2.0]"/>
81 <param name="chimeric_overlap" type="integer" value="2" 82 <param argument="--chimeric_overlap" type="integer" value="2"
82 label=" Maximum number of bases allowed between the chimericsegments of a read"/> 83 label=" Maximum number of bases allowed between the chimericsegments of a read"/>
83 <conditional name="reference"> 84 <conditional name="reference">
84 <param name="ref_type" type="select" label="Did you use single or split reference for alignment?"> 85 <param name="ref_type" type="select" label="Did you use single or split reference for alignment?">
85 <option value="split">Split reference</option> 86 <option value="split">Split reference</option>
86 <option value="single">Single reference</option> 87 <option value="single">Single reference</option>
87 </param> 88 </param>
88 <when value="split"> 89 <when value="split">
89 <param format="fasta" name="ref_fasta1" type="data" label="Reference FASTA file" 90 <param format="fasta" argument="--ref_fasta1" type="data" label="Reference FASTA file"
90 help="Reference fasta file"/> 91 help="Reference fasta file"/>
91 <param format="fasta" name="ref_fasta2" type="data" label="Second reference FASTA file" 92 <param format="fasta" argument="--ref_fasta2" type="data" label="Second reference FASTA file"
92 help="Second reference fasta file."/> 93 help="Second reference fasta file."/>
93 </when> 94 </when>
94 <when value="single"> 95 <when value="single">
95 <param format="fasta" name="ref_fasta" type="data" label="Reference FASTA file" 96 <param format="fasta" argument="--ref_fasta1" name="ref_fasta" type="data" label="Reference FASTA file"
96 help="Reference fasta file"/> 97 help="Reference fasta file"/>
97 </when> 98 </when>
98 </conditional> 99 </conditional>
99 <param name="hybridize" type="boolean" truevalue="-r" falsevalue="" checked="false" 100 <param argument="--hybridize" type="boolean" truevalue="-r" falsevalue="" checked="false"
100 label="Hybridize chimeric loci?" 101 label="Hybridize chimeric loci?"
101 help="Turning this option on increases the run time of the tool significantly."/> 102 help="Turning this option on increases the run time of the tool significantly."/>
102 <param name="intarna_mode" type="select"> 103 <param argument="--intarna_mode" type="select">
103 <option value="H">Heuristic</option> 104 <option value="H">Heuristic</option>
104 <option value="M">Exact</option> 105 <option value="M">Exact</option>
105 <option value="S">Seed-only</option> 106 <option value="S">Seed-only</option>
106 </param> 107 </param>
107 <param name="seed_interaction" type="boolean" truevalue="" falsevalue="--no_seed" checked="true" 108 <param argument="--no_seed" name="seed_interaction" type="boolean" truevalue="" falsevalue="--no_seed" checked="true"
108 label="Enforce seed interaction?"/> 109 label="Enforce seed interaction?"/>
109 <param name="seed_bp" type="integer" value="5" min="2" max="20" 110 <param argument="--seed_bp" type="integer" value="5" min="2" max="20"
110 label="Number of inter-molecular base pairs within the seed region" 111 label="Number of inter-molecular base pairs within the seed region"
111 help="IntaRNA --seedBP parameter"/> 112 help="IntaRNA --seedBP parameter"/>
112 <param name="seed_min_pu" type="float" value="0" min="0" max="1" 113 <param argument="--seed_min_pu" type="float" value="0" min="0" max="1"
113 label="Minimal unpaired probability (per sequence) a seed region may have" 114 label="Minimal unpaired probability (per sequence) a seed region may have"
114 help="IntaRNA --seedMinPu parameter"/> 115 help="IntaRNA --seedMinPu parameter"/>
115 <param name="accessibility" type="boolean" truevalue="C" falsevalue="N" checked="false" 116 <param argument="--accessibility" type="boolean" truevalue="C" falsevalue="N" checked="false"
116 label="Compute accessibility profiles for interacting sequences?"/> 117 label="Compute accessibility profiles for interacting sequences?"/>
117 <param name="acc_width" type="integer" value="150" min="0" max="99999" 118 <param argument="--acc_width" type="integer" value="150" min="0" max="99999"
118 label="Sliding window size for accessibility computation" 119 label="Sliding window size for accessibility computation"
119 help="IntaRNA --accW parameter"/> 120 help="IntaRNA --accW parameter"/>
120 <param name="temperature" type="float" value="37" min="0" max="100" 121 <param argument="--temperature" type="float" value="37" min="0" max="100"
121 label="IntaRNA temperature parameter in Celsius to setup the VRNA energy parameters"/> 122 label="IntaRNA temperature parameter in Celsius to setup the VRNA energy parameters"/>
122 <param name="summarize" type="boolean" truevalue="-s" falsevalue="" checked="false" 123 <param argument="--summerize" name="summarize" type="boolean" truevalue="-s" falsevalue="" checked="false"
123 label="Summarize interactions at loci level?"/> 124 label="Summarize interactions at loci level?"/>
124 </inputs> 125 </inputs>
125 126
126 <outputs> 127 <outputs>
127 <data format="tabular" name="chimeras" from_work_dir="chimeras" label="ChiRA chimeric reads on ${on_string}"/> 128 <data format="tabular" name="chimeras" from_work_dir="chimeras" label="ChiRA chimeric reads on ${on_string}"/>