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comparison mircounts.xml @ 4:da1aa7de2b19 draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit ddaf9622722487d010001cd1f255107adf0c332d
author artbio
date Mon, 04 Sep 2017 17:55:01 -0400
parents 6b8adacd4750
children 9ea96a02c416
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3:6b8adacd4750 4:da1aa7de2b19
1 <tool id="mircounts" name="miRcounts" version="0.9.3"> 1 <tool id="mircounts" name="miRcounts" version="0.9.4">
2 <description> Counts miRNA alignments from small RNA sequence data</description> 2 <description> Counts miRNA alignments from small RNA sequence data</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.18">gnu-wget</requirement> 4 <requirement type="package" version="1.18">gnu-wget</requirement>
5 <requirement type="package" version="1.2">bowtie</requirement> 5 <requirement type="package" version="1.2">bowtie</requirement>
6 <requirement type="package" version="1.4.1">samtools</requirement> 6 <requirement type="package" version="1.4.1">samtools</requirement>
7 <requirement type="package" version="0.11.2.1">pysam</requirement> 7 <requirement type="package" version="0.11.2.1">pysam</requirement>
8 <requirement type="package" version="1.3.2=r3.3.2_0">r-optparse</requirement> 8 <requirement type="package" version="1.3.2=r3.3.2_0">r-optparse</requirement>
9 <requirement type="package" version="0.20_34=r3.3.2_0">r-lattice</requirement> 9 <requirement type="package" version="0.20_34=r3.3.2_0">r-lattice</requirement>
10 </requirements> 10 </requirements>
11 <command detect_errors="exit_code"><![CDATA[ 11 <command detect_errors="exit_code"><![CDATA[
12 ## To be refactored with guidelines in https://github.com/ARTbio/tools-artbio/issues/140
13 wget ftp://mirbase.org/pub/mirbase/CURRENT/genomes/${genomeKey}.gff3 && ## download gff3 specified by the variable genomeKey 12 wget ftp://mirbase.org/pub/mirbase/CURRENT/genomes/${genomeKey}.gff3 && ## download gff3 specified by the variable genomeKey
14 python '$__tool_directory__'/mature_mir_gff_translation.py --input ${genomeKey}.gff3 --output $gff3 && ## transcode the mature miR genome coordinates into coordinates relative to the corresponding "miRNA_primary_transcript". 13 python '$__tool_directory__'/mature_mir_gff_translation.py --input ${genomeKey}.gff3 --output $gff3 && ## transcode the mature miR genome coordinates into coordinates relative to the corresponding "miRNA_primary_transcript".
15 wget ftp://mirbase.org/pub/mirbase/CURRENT/hairpin.fa.gz && 14 wget ftp://mirbase.org/pub/mirbase/CURRENT/hairpin.fa.gz &&
16 sh '$__tool_directory__'/format_fasta_hairpins.sh $genomeKey && 15 sh '$__tool_directory__'/format_fasta_hairpins.sh $genomeKey &&
17 #if $cutadapt.cutoption == "yes": 16 #if $cutadapt.cutoption == "yes":
73 <options from_data_table="miRbase_GenomeKeys"> 72 <options from_data_table="miRbase_GenomeKeys">
74 <column name="name" index="1"/> 73 <column name="name" index="1"/>
75 <column name="value" index="0"/> 74 <column name="value" index="0"/>
76 </options> 75 </options>
77 </param> 76 </param>
77 <!-- work on proper selection of the url (that varies between gff, gff2 and gff3)
78 <param name="mirbase_version" type="select" label="Choose miRbase version">
79 <option selected="true" value="CURRENT">Current</option>
80 <option value="1.0">1.0</option>
81 <option value="1.1">1.1</option>
82 <option value="1.2">1.2</option>
83 <option value="1.3">1.3</option>
84 <option value="1.4">1.4</option>
85 <option value="1.5">1.5</option>
86 <option value="2.0">2.0</option>
87 <option value="2.1">2.0</option>
88 <option value="2.2">2.2</option>
89 <option value="3.0">3.0</option>
90 <option value="3.1">3.1</option>
91 <option value="4.0">4.0</option>
92 <option value="5.0">5.0</option>
93 <option value="5.1">5.1</option>
94 <option value="6.0">6.0</option>
95 <option value="7.0">7.0</option>
96 <option value="7.1">7.1</option>
97 <option value="8.0">8.0</option>
98 <option value="8.1">8.1</option>
99 <option value="8.2">8.2</option>
100 <option value="9.0">9.0</option>
101 <option value="9.1">9.1</option>
102 <option value="9.2">9.2</option>
103 <option value="10.0">10.0</option>
104 <option value="10.1">10.1</option>
105 <option value="11.0">11.0</option>
106 <option value="12.0">12.0</option>
107 <option value="13.0">13.0</option>
108 <option value="14">14</option>
109 <option value="15">15</option>
110 <option value="16">16</option>
111 <option value="17">17</option>
112 <option value="18">18</option>
113 <option value="19">19</option>
114 <option value="20">20</option>
115 <option value="21">21</option>
116 </options>
117 </param>
118 -->
78 <param help="command [ bowtie -v 0,1,2,3 -M 1 --best --strata --norc ] will be used. Specify a value for -v (number of mismatches allowed)" label="Number of mismatches allowed" name="v" type="select"> 119 <param help="command [ bowtie -v 0,1,2,3 -M 1 --best --strata --norc ] will be used. Specify a value for -v (number of mismatches allowed)" label="Number of mismatches allowed" name="v" type="select">
79 <option value="0">0</option> 120 <option value="0">0</option>
80 <option selected="true" value="1">1</option> 121 <option selected="true" value="1">1</option>
81 <option value="2">2</option> 122 <option value="2">2</option>
82 <option value="3">3</option> 123 <option value="3">3</option>
97 </conditional> 138 </conditional>
98 </inputs> 139 </inputs>
99 <outputs> 140 <outputs>
100 <data format="bam" label="BAM alignment" name="output" /> 141 <data format="bam" label="BAM alignment" name="output" />
101 <data format="gff3" label="GFF3 generated by miRCounts" name="gff3"/> 142 <data format="gff3" label="GFF3 generated by miRCounts" name="gff3"/>
102 <data format="tabular" label="Pre-mir Counts" name="pre_mir_count_file" /> 143 <data format="tabular" label="Pre-mir Counts" name="pre_mir_count_file">
103 <data format="tabular" label="Mir Counts" name="mir_count_file" /> 144 <actions>
145 <action name="column_names" type="metadata" default="Gene,Counts" />
146 </actions>
147 </data>
148 <data format="tabular" label="Mir Counts" name="mir_count_file">
149 <actions>
150 <action name="column_names" type="metadata" default="Gene,Counts" />
151 </actions>
152 </data>
104 <data format="tabular" label="Coverage Table" name="coverage_dataframe"> 153 <data format="tabular" label="Coverage Table" name="coverage_dataframe">
105 <filter>plotting['plottingOption'] == "yes"</filter> 154 <filter>plotting['plottingOption'] == "yes"</filter>
106 </data> 155 </data>
107 <data format="pdf" label="Pre-mir coverage (${plotting.display})" name="latticePDF"> 156 <data format="pdf" label="Pre-mir coverage (${plotting.display})" name="latticePDF">
108 <filter>plotting['plottingOption'] == "yes"</filter> 157 <filter>plotting['plottingOption'] == "yes"</filter>