Mercurial > repos > artbio > sr_bowtie_dataset_annotation

comparison sr_bowtie_dataset_annotation.xml @ 8:3519c2de7fac draft

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"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit e62066428e669516e024d081933ee8c7f953ba1b"
author artbio
date Sat, 09 Apr 2022 22:45:21 +0000
parents 3bddd7ab96e3
children 6bf9de09aa74
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7:3bddd7ab96e3 8:3519c2de7fac
1 <tool id="sr_bowtie_dataset_annotation" name="Annotate smRNA dataset" version="2.5.0"> 1 <tool id="sr_bowtie_dataset_annotation" name="Annotate smRNA dataset" version="2.6">
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>
57 rm tmp_class_matched.fa && 57 rm tmp_class_matched.fa &&
58 #end for 58 #end for
59 remaining=\$(( \$(wc -l < class_unmatched.fa)/2)) && 59 remaining=\$(( \$(wc -l < class_unmatched.fa)/2)) &&
60 echo -e "$sample\tNot classified\t\${remaining}\t\${genome_aligned}" >> $output && 60 echo -e "$sample\tNot classified\t\${remaining}\t\${genome_aligned}" >> $output &&
61 #end for 61 #end for
62
63
64 Rscript $__tool_directory__/barplot.r --input $output --barplot $barplot 62 Rscript $__tool_directory__/barplot.r --input $output --barplot $barplot
63 #if $format == '-q':
64 && mv class_unmatched.fa class_unmatched.fastq
65 && sed -n '1~4s/^@/>/p;2~4p' class_unmatched.fastq > class_unmatched.fa
66 #end if
65 ]]></command> 67 ]]></command>
66 <inputs> 68 <inputs>
67 <param name="input" type="data" multiple="True" format="fasta,fastq" label="Input file: reads clipped from their adapter" help="Only with clipped, raw fasta or fastq files"/> 69 <param name="input" type="data" multiple="True" format="fasta,fastq" label="Input file: reads clipped from their adapter" help="Only with clipped, raw fasta or fastq files"/>
68 <param name="mismatches" type="select" label="Number of mismatches allowed" help="specify the number of mismatches allowed during alignments"> 70 <param name="mismatches" type="select" label="Number of mismatches allowed" help="specify the number of mismatches allowed during alignments">
69 <option value="0">0</option> 71 <option value="0">0</option>
92 <param name="ownFile" type="data" format="fasta" label="Select a fasta file, to serve as index reference" /> 94 <param name="ownFile" type="data" format="fasta" label="Select a fasta file, to serve as index reference" />
93 </repeat> 95 </repeat>
94 <!-- End of other bowtie index selections --> 96 <!-- End of other bowtie index selections -->
95 </inputs> 97 </inputs>
96 <outputs> 98 <outputs>
99 <data format="fasta" name="unmatched" label="Annotate smRNAs: Unmatched reads" from_work_dir="class_unmatched.fa" />
97 <data format="tabular" name="output" label="Cascade Annotation Analysis"> 100 <data format="tabular" name="output" label="Cascade Annotation Analysis">
98 <actions> 101 <actions>
99 <action name="column_names" type="metadata" default="Sample,Reference Index,Number of reads, Total reads" /> 102 <action name="column_names" type="metadata" default="Sample,Reference Index,Number of reads, Total reads" />
100 </actions> 103 </actions>
101 </data> 104 </data>
108 <param name="ownFile" value ="2L-tail.fa" ftype="fasta" /> 111 <param name="ownFile" value ="2L-tail.fa" ftype="fasta" />
109 <param name="AdditionalQueries_0|ownFile" value="dme_miR21_hairpin.fa" ftype="fasta" /> 112 <param name="AdditionalQueries_0|ownFile" value="dme_miR21_hairpin.fa" ftype="fasta" />
110 <param name="AdditionalQueries_1|ownFile" value="Ensembl_transposon_set.fa" ftype="fasta" /> 113 <param name="AdditionalQueries_1|ownFile" value="Ensembl_transposon_set.fa" ftype="fasta" />
111 <output name="output" ftype="tabular" file="sample1_output.tab" /> 114 <output name="output" ftype="tabular" file="sample1_output.tab" />
112 <output name="barplot" ftype="pdf" file="sample1_output.pdf" compare="sim_size" delta="500"/> 115 <output name="barplot" ftype="pdf" file="sample1_output.pdf" compare="sim_size" delta="500"/>
116 <output name="unmatched" ftype="fasta" file="unmatched_1.fa" />
113 </test> 117 </test>
114 <test> 118 <test>
115 <param name="input" value ="sample.fastq" ftype="fastq" /> 119 <param name="input" value ="sample.fastq" ftype="fastq" />
116 <param name="genomeSource" value="history" /> 120 <param name="genomeSource" value="history" />
117 <param name="ownFile" value ="2L-tail.fa" ftype="fasta" /> 121 <param name="ownFile" value ="2L-tail.fa" ftype="fasta" />
118 <param name="AdditionalQueries_0|ownFile" value="dme_miR21_hairpin.fa" ftype="fasta" /> 122 <param name="AdditionalQueries_0|ownFile" value="dme_miR21_hairpin.fa" ftype="fasta" />
119 <param name="AdditionalQueries_1|ownFile" value="Ensembl_transposon_set.fa" ftype="fasta" /> 123 <param name="AdditionalQueries_1|ownFile" value="Ensembl_transposon_set.fa" ftype="fasta" />
120 <output name="output" ftype="tabular" file="sample_output.tab" /> 124 <output name="output" ftype="tabular" file="sample_output.tab" />
121 <output name="barplot" ftype="pdf" file="sample_output.pdf" compare="sim_size" delta="500"/> 125 <output name="barplot" ftype="pdf" file="sample_output.pdf" compare="sim_size" delta="500"/>
126 <output name="unmatched" ftype="fasta" file="unmatched_2.fa" />
122 </test> 127 </test>
123 <test> 128 <test>
124 <param name="input" value ="sample5.fa,sample4.fa,sample3.fa,sample2.fa,sample1.fa" ftype="fasta" /> 129 <param name="input" value ="sample5.fa,sample4.fa,sample3.fa,sample2.fa,sample1.fa" ftype="fasta" />
125 <param name="genomeSource" value="history" /> 130 <param name="genomeSource" value="history" />
126 <param name="ownFile" value ="2L-tail.fa" ftype="fasta" /> 131 <param name="ownFile" value ="2L-tail.fa" ftype="fasta" />
127 <param name="AdditionalQueries_0|ownFile" value="dme_miR21_hairpin.fa" ftype="fasta" /> 132 <param name="AdditionalQueries_0|ownFile" value="dme_miR21_hairpin.fa" ftype="fasta" />
128 <param name="AdditionalQueries_1|ownFile" value="Ensembl_transposon_set.fa" ftype="fasta" /> 133 <param name="AdditionalQueries_1|ownFile" value="Ensembl_transposon_set.fa" ftype="fasta" />
129 <output name="output" ftype="tabular" file="multisample5_output.tab" /> 134 <output name="output" ftype="tabular" file="multisample5_output.tab" />
130 <output name="barplot" ftype="pdf" file="multisample5_output.pdf" compare="sim_size" delta="500" /> 135 <output name="barplot" ftype="pdf" file="multisample5_output.pdf" compare="sim_size" delta="500" />
136 <output name="unmatched" ftype="fasta" file="unmatched_3.fa" />
131 </test> 137 </test>
132 </tests> 138 </tests>
133 <help> 139 <help>
134 140
135 **Introduction** 141 **Introduction**
170 176
171 ----- 177 -----
172 178
173 **OUTPUTS** 179 **OUTPUTS**
174 180
175 **Annotation table in a tabular format** 181 **- Annotation table in a tabular format**
182
183 **- Pie Charts of class abundances**
184
185 **- Unmatched reads in fasta format**
176 186
177 </help> 187 </help>
188
189 <citations>
190 <citation type="doi">10.1038/nature11416</citation>
191 </citations>
192
178 </tool> 193 </tool>