Mercurial > repos > artbio > mircounts

comparison mircounts.xml @ 5:9ea96a02c416 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 04980585c257ab5f8eb5d10de007316c47c5d1ce
author artbio
date Tue, 05 Sep 2017 06:33:16 -0400
parents da1aa7de2b19
children 543472c9e272
comparison
equal deleted inserted replaced
4:da1aa7de2b19 5:9ea96a02c416
1 <tool id="mircounts" name="miRcounts" version="0.9.4"> 1 <tool id="mircounts" name="miRcounts" version="1.0.0">
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 wget ftp://mirbase.org/pub/mirbase/CURRENT/genomes/${genomeKey}.gff3 && ## download gff3 specified by the variable genomeKey 12 wget ftp://mirbase.org/pub/mirbase/${mirbase_version}/genomes/${genomeKey}.gff3 && ## download the gff3 file specified by the variable genomeKey
13 python '$__tool_directory__'/mature_mir_gff_translation.py --input ${genomeKey}.gff3 --output $gff3 && ## transcode the mature miR genome coordinates into coordinates relative to the corresponding "miRNA_primary_transcript". 13 python '$__tool_directory__'/mature_mir_gff_translation.py --input ${genomeKey}.gff3 --output $gff3 && ## transcode the mature miR genome coordinates into coordinates relative to the corresponding "miRNA_primary_transcript".
14 wget ftp://mirbase.org/pub/mirbase/CURRENT/hairpin.fa.gz && 14 wget ftp://mirbase.org/pub/mirbase/${mirbase_version}/hairpin.fa.gz &&
15 sh '$__tool_directory__'/format_fasta_hairpins.sh $genomeKey && 15 sh '$__tool_directory__'/format_fasta_hairpins.sh $genomeKey &&
16 #if $cutadapt.cutoption == "yes": 16 #if $cutadapt.cutoption == "yes":
17 python '$__tool_directory__'/yac.py --input $cutadapt.input 17 python '$__tool_directory__'/yac.py --input $cutadapt.input
18 --output clipped_input.fastq 18 --output clipped_input.fastq
19 --output_format fastq 19 --output_format fastq
72 <options from_data_table="miRbase_GenomeKeys"> 72 <options from_data_table="miRbase_GenomeKeys">
73 <column name="name" index="1"/> 73 <column name="name" index="1"/>
74 <column name="value" index="0"/> 74 <column name="value" index="0"/>
75 </options> 75 </options>
76 </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"> 77 <param name="mirbase_version" type="select" label="Choose miRbase version">
79 <option selected="true" value="CURRENT">Current</option> 78 <option selected="true" value="CURRENT">Current</option>
80 <option value="1.0">1.0</option> 79 <option value="20">20</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> 80 <option value="19">19</option>
114 <option value="20">20</option>
115 <option value="21">21</option>
116 </options>
117 </param> 81 </param>
118 -->
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"> 82 <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">
120 <option value="0">0</option> 83 <option value="0">0</option>
121 <option selected="true" value="1">1</option> 84 <option selected="true" value="1">1</option>
122 <option value="2">2</option> 85 <option value="2">2</option>
123 <option value="3">3</option> 86 <option value="3">3</option>
164 <param name="max" value="25"/> 127 <param name="max" value="25"/>
165 <param name="Nmode" value="reject"/> 128 <param name="Nmode" value="reject"/>
166 <param name="clip_sequence" value="TCGTATGCCGTCTTCTGCTTG"/> 129 <param name="clip_sequence" value="TCGTATGCCGTCTTCTGCTTG"/>
167 <param name="v" value="0"/> 130 <param name="v" value="0"/>
168 <param name="genomeKey" value="dme"/> 131 <param name="genomeKey" value="dme"/>
132 <param name="mirbase_version" value="CURRENT"/>
169 <param name="input" value="input.unclipped.fastqsanger" ftype="fastqsanger"/> 133 <param name="input" value="input.unclipped.fastqsanger" ftype="fastqsanger"/>
170 <param name="plottingOption" value="no"/> 134 <param name="plottingOption" value="no"/>
171 <output name="output" file="unclipped.out.bam" ftype="bam"/> 135 <output name="output" file="unclipped.out.bam" ftype="bam"/>
172 <output name="gff3" file="translated_dme.gff3" ftype="gff3"/> 136 <output name="gff3" file="translated_dme.gff3" ftype="gff3" lines_diff="22"/>
173 <output name="pre_mir_count_file" file="pre_mirs_unclipped_count.tab"/> 137 <output name="pre_mir_count_file" file="pre_mirs_unclipped_count.tab"/>
174 <output name="mir_count_file" file="mirs_unclipped_count.tab"/> 138 <output name="mir_count_file" file="mirs_unclipped_count.tab"/>
175 </test> 139 </test>
176 <test> 140 <test>
177 <param name="cutoption" value="yes" /> 141 <param name="cutoption" value="yes" />
179 <param name="max" value="25"/> 143 <param name="max" value="25"/>
180 <param name="Nmode" value="reject"/> 144 <param name="Nmode" value="reject"/>
181 <param name="clip_sequence" value="TCGTATGCCGTCTTCTGCTTG"/> 145 <param name="clip_sequence" value="TCGTATGCCGTCTTCTGCTTG"/>
182 <param name="v" value="0"/> 146 <param name="v" value="0"/>
183 <param name="genomeKey" value="dme"/> 147 <param name="genomeKey" value="dme"/>
148 <param name="mirbase_version" value="CURRENT"/>
184 <param name="input" value="input.unclipped.fastqsanger" ftype="fastqsanger"/> 149 <param name="input" value="input.unclipped.fastqsanger" ftype="fastqsanger"/>
185 <param name="plottingOption" value="yes"/> 150 <param name="plottingOption" value="yes"/>
186 <param name="display" value="relative"/> 151 <param name="display" value="relative"/>
187 <output name="output" file="unclipped.out.bam" ftype="bam"/> 152 <output name="output" file="unclipped.out.bam" ftype="bam"/>
188 <output name="gff3" file="translated_dme.gff3" ftype="gff3"/> 153 <output name="gff3" file="translated_dme.gff3" ftype="gff3" lines_diff="22"/>
189 <output name="pre_mir_count_file" file="pre_mirs_unclipped_count.tab"/> 154 <output name="pre_mir_count_file" file="pre_mirs_unclipped_count.tab"/>
190 <output name="mir_count_file" file="mirs_unclipped_count.tab"/> 155 <output name="mir_count_file" file="mirs_unclipped_count.tab"/>
191 <output name="latticePDF" file="mir_unclipped_coverage.pdf" ftype="pdf"/> 156 <output name="latticePDF" file="mir_unclipped_coverage.pdf" ftype="pdf"/>
192 <output name="coverage_dataframe" file="lattice_unclipped_dataframe.tab"/> 157 <output name="coverage_dataframe" file="lattice_unclipped_dataframe.tab"/>
193 </test> 158 </test>
194 <test> 159 <test>
195 <param name="cutoption" value="no" /> 160 <param name="cutoption" value="no" />
196 <param name="v" value="1"/> 161 <param name="v" value="1"/>
197 <param name="genomeKey" value="dme"/> 162 <param name="genomeKey" value="dme"/>
163 <param name="mirbase_version" value="CURRENT"/>
198 <param name="clipped_input" value="input.clipped.fastqsanger" ftype="fastqsanger"/> 164 <param name="clipped_input" value="input.clipped.fastqsanger" ftype="fastqsanger"/>
199 <param name="plottingOption" value="yes"/> 165 <param name="plottingOption" value="yes"/>
200 <param name="display" value="absolute"/> 166 <param name="display" value="absolute"/>
201 <output name="output" file="clipped.out.bam" ftype="bam"/> 167 <output name="output" file="clipped.out.bam" ftype="bam"/>
202 <output name="gff3" file="translated_dme.gff3" ftype="gff3"/> 168 <output name="gff3" file="translated_dme.gff3" ftype="gff3" lines_diff="22"/>
203 <output name="pre_mir_count_file" file="pre_mirs_clipped_count.tab"/> 169 <output name="pre_mir_count_file" file="pre_mirs_clipped_count.tab"/>
204 <output name="mir_count_file" file="mirs_clipped_count.tab"/> 170 <output name="mir_count_file" file="mirs_clipped_count.tab"/>
205 <output name="latticePDF" file="mir_clipped_coverage.pdf" ftype="pdf"/> 171 <output name="latticePDF" file="mir_clipped_coverage.pdf" ftype="pdf"/>
206 <output name="coverage_dataframe" file="lattice_clipped_dataframe.tab"/> 172 <output name="coverage_dataframe" file="lattice_clipped_dataframe.tab"/>
207 </test> 173 </test>