Mercurial > repos > artbio > sr_bowtie_dataset_annotation

comparison sr_bowtie_dataset_annotation.xml @ 10:fd4a60fc3fca draft default tip

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit cf30b4fab90cf7910bb2900a05b85ca3344aae59
author artbio
date Tue, 15 Nov 2022 00:45:36 +0000
parents 6bf9de09aa74
children
comparison
equal deleted inserted replaced
9:6bf9de09aa74 10:fd4a60fc3fca
1 <tool id="sr_bowtie_dataset_annotation" name="Annotate smRNA dataset" version="2.7"> 1 <tool id="sr_bowtie_dataset_annotation" name="Annotate smRNA dataset" version="2.8">
2 <description>by iterative alignments with sRbowtie</description> 2 <description>by iterative alignments with sRbowtie</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.3.1">bowtie</requirement> 4 <requirement type="package" version="1.3.1">bowtie</requirement>
5 <requirement type="package" version="1.7.1">r-optparse</requirement> 5 <requirement type="package" version="1.7.1">r-optparse</requirement>
6 <requirement type="package" version="3.3.5">r-ggplot2</requirement> 6 <requirement type="package" version="3.3.5">r-ggplot2</requirement>
7 <requirement type="package" version="0.9.1">r-ggrepel</requirement> 7 <requirement type="package" version="0.9.1">r-ggrepel</requirement>
8 </requirements> 8 </requirements>
9 <command detect_errors="exit_code"><![CDATA[ 9 <command detect_errors="exit_code"><![CDATA[
10 #if $refGenomeSource1.genomeSource == "history": 10 #if $refGenomeSource1.genomeSource == "history":
11 bowtie-build -f $refGenomeSource1.ownFile genome 1>/dev/null && 11 bowtie-build --threads \${GALAXY_SLOTS:-4} -f $refGenomeSource1.ownFile genome 1>/dev/null &&
12 #set index_path = 'genome' 12 #set index_path = 'genome'
13 #else: 13 #else:
14 #set index_path = $refGenomeSource1.index.fields.path 14 #set index_path = $refGenomeSource1.index.fields.path
15 #end if 15 #end if
16 16
17 #for $i in $AdditionalQueries: 17 #for $i in $AdditionalQueries:
18 bowtie-build -f $i.ownFile $i.ownFile.name 1>/dev/null && 18 bowtie-build --threads \${GALAXY_SLOTS:-4} -f $i.ownFile $i.ownFile.name 1>/dev/null &&
19 #end for 19 #end for
20 20
21 #set method_prefix = "-v %s -k 1 --best" % str($mismatches) 21 #set method_prefix = "-v %s -k 1 --best" % str($mismatches)
22 #if $input[0].is_of_type('fasta'): 22 #if $input[0].is_of_type('fasta'):
23 #set format = "-f" 23 #set format = "-f"
119 <param name="AdditionalQueries_0|ownFile" value="dme_miR21_hairpin.fa" ftype="fasta" /> 119 <param name="AdditionalQueries_0|ownFile" value="dme_miR21_hairpin.fa" ftype="fasta" />
120 <param name="AdditionalQueries_1|ownFile" value="Ensembl_transposon_set.fa" ftype="fasta" /> 120 <param name="AdditionalQueries_1|ownFile" value="Ensembl_transposon_set.fa" ftype="fasta" />
121 <output name="output" ftype="tabular" file="multisample5_output.tab" /> 121 <output name="output" ftype="tabular" file="multisample5_output.tab" />
122 <output name="barplot" ftype="pdf" file="multisample5_output.pdf" compare="sim_size" delta="500" /> 122 <output name="barplot" ftype="pdf" file="multisample5_output.pdf" compare="sim_size" delta="500" />
123 <output_collection name="unmatched" type="list" count="5"> 123 <output_collection name="unmatched" type="list" count="5">
124 <element name="sample5.fa_unmatched" file="unmatched_5.fa" ftype="fasta"/> 124 <element name="sample5.fa_unmatched" file="unmatched_5.fa" ftype="fasta" compare="sim_size" delta="0"/>
125 <element name="sample4.fa_unmatched" file="unmatched_4.fa" ftype="fasta"/> 125 <element name="sample4.fa_unmatched" file="unmatched_4.fa" ftype="fasta" compare="sim_size" delta="0"/>
126 <element name="sample3.fa_unmatched" file="unmatched_3.fa" ftype="fasta"/> 126 <element name="sample3.fa_unmatched" file="unmatched_3.fa" ftype="fasta" compare="sim_size" delta="0"/>
127 <element name="sample2.fa_unmatched" file="unmatched_2.fa" ftype="fasta"/> 127 <element name="sample2.fa_unmatched" file="unmatched_2.fa" ftype="fasta" compare="sim_size" delta="0"/>
128 <element name="sample1.fa_unmatched" file="unmatched_1.fa" ftype="fasta"/> 128 <element name="sample1.fa_unmatched" file="unmatched_1.fa" ftype="fasta" compare="sim_size" delta="0"/>
129 </output_collection> 129 </output_collection>
130 </test> 130 </test>
131 <test> 131 <test>
132 <param name="input" value ="sample1.fa" ftype="fasta" /> 132 <param name="input" value ="sample1.fa" ftype="fasta" />
133 <param name="genomeSource" value="history" /> 133 <param name="genomeSource" value="history" />
135 <param name="AdditionalQueries_0|ownFile" value="dme_miR21_hairpin.fa" ftype="fasta" /> 135 <param name="AdditionalQueries_0|ownFile" value="dme_miR21_hairpin.fa" ftype="fasta" />
136 <param name="AdditionalQueries_1|ownFile" value="Ensembl_transposon_set.fa" ftype="fasta" /> 136 <param name="AdditionalQueries_1|ownFile" value="Ensembl_transposon_set.fa" ftype="fasta" />
137 <output name="output" ftype="tabular" file="sample1_output.tab" /> 137 <output name="output" ftype="tabular" file="sample1_output.tab" />
138 <output name="barplot" ftype="pdf" file="sample1_output.pdf" compare="sim_size" delta="500"/> 138 <output name="barplot" ftype="pdf" file="sample1_output.pdf" compare="sim_size" delta="500"/>
139 <output_collection name="unmatched" type="list"> 139 <output_collection name="unmatched" type="list">
140 <element name="sample1.fa_unmatched" file="unmatched_1.fa" ftype="fasta"/> 140 <element name="sample1.fa_unmatched" file="unmatched_6.fa" ftype="fasta" compare="sim_size" delta="0"/>
141 </output_collection> 141 </output_collection>
142 </test> 142 </test>
143 <test> 143 <test>
144 <param name="input" value ="sample.fastq" ftype="fastq" /> 144 <param name="input" value ="sample.fastq" ftype="fastq" />
145 <param name="genomeSource" value="history" /> 145 <param name="genomeSource" value="history" />