Mercurial > repos > artbio > sr_bowtie_dataset_annotation

comparison sr_bowtie_dataset_annotation.xml @ 9:6bf9de09aa74 draft

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"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit c8f13ba73552ccf7db7c22859b7fdc6ad121cdf0"
author artbio
date Mon, 11 Apr 2022 00:27:41 +0000
parents 3519c2de7fac
children fd4a60fc3fca
comparison
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8:3519c2de7fac 9:6bf9de09aa74
1 <tool id="sr_bowtie_dataset_annotation" name="Annotate smRNA dataset" version="2.6"> 1 <tool id="sr_bowtie_dataset_annotation" name="Annotate smRNA dataset" version="2.7">
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>
22 #if $input[0].is_of_type('fasta'): 22 #if $input[0].is_of_type('fasta'):
23 #set format = "-f" 23 #set format = "-f"
24 #elif $input[0].is_of_type('fastq'): 24 #elif $input[0].is_of_type('fastq'):
25 #set format = "-q" 25 #set format = "-q"
26 #end if 26 #end if
27 27
28 mkdir unmatched_dir &&
29
28 #for $file in $input: 30 #for $file in $input:
29 #set sample=$file.element_identifier 31 #set sample=$file.element_identifier
30 bowtie -p \${GALAXY_SLOTS:-4} 32 bowtie -p \${GALAXY_SLOTS:-4}
31 $method_prefix 33 $method_prefix
32 --al matched.fa 34 --al matched.fa
56 mv tmp_class_unmatched.fa class_unmatched.fa && 58 mv tmp_class_unmatched.fa class_unmatched.fa &&
57 rm tmp_class_matched.fa && 59 rm tmp_class_matched.fa &&
58 #end for 60 #end for
59 remaining=\$(( \$(wc -l < class_unmatched.fa)/2)) && 61 remaining=\$(( \$(wc -l < class_unmatched.fa)/2)) &&
60 echo -e "$sample\tNot classified\t\${remaining}\t\${genome_aligned}" >> $output && 62 echo -e "$sample\tNot classified\t\${remaining}\t\${genome_aligned}" >> $output &&
63 cp class_unmatched.fa unmatched_dir/${sample}_unmatched.fasta &&
64 #if $format == '-q':
65 mv unmatched_dir/${sample}_unmatched.fasta unmatched_dir/${sample}_unmatched.fastq &&
66 sed -n '1~4s/^@/>/p;2~4p' unmatched_dir/${sample}_unmatched.fastq > unmatched_dir/${sample}_unmatched.fasta &&
67 rm unmatched_dir/${sample}_unmatched.fastq &&
68 #end if
61 #end for 69 #end for
70 ls -la unmatched_dir &&
62 Rscript $__tool_directory__/barplot.r --input $output --barplot $barplot 71 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
67 ]]></command> 72 ]]></command>
68 <inputs> 73 <inputs>
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"/> 74 <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"/>
70 <param name="mismatches" type="select" label="Number of mismatches allowed" help="specify the number of mismatches allowed during alignments"> 75 <param name="mismatches" type="select" label="Number of mismatches allowed" help="specify the number of mismatches allowed during alignments">
71 <option value="0">0</option> 76 <option value="0">0</option>
94 <param name="ownFile" type="data" format="fasta" label="Select a fasta file, to serve as index reference" /> 99 <param name="ownFile" type="data" format="fasta" label="Select a fasta file, to serve as index reference" />
95 </repeat> 100 </repeat>
96 <!-- End of other bowtie index selections --> 101 <!-- End of other bowtie index selections -->
97 </inputs> 102 </inputs>
98 <outputs> 103 <outputs>
99 <data format="fasta" name="unmatched" label="Annotate smRNAs: Unmatched reads" from_work_dir="class_unmatched.fa" /> 104 <collection name="unmatched" type="list" format="fasta" label="Annotate smRNAs: Unmatched reads">
105 <discover_datasets pattern="__name_and_ext__" directory="unmatched_dir" />
106 </collection>
100 <data format="tabular" name="output" label="Cascade Annotation Analysis"> 107 <data format="tabular" name="output" label="Cascade Annotation Analysis">
101 <actions> 108 <actions>
102 <action name="column_names" type="metadata" default="Sample,Reference Index,Number of reads, Total reads" /> 109 <action name="column_names" type="metadata" default="Sample,Reference Index,Number of reads, Total reads" />
103 </actions> 110 </actions>
104 </data> 111 </data>
105 <data name="barplot" format="pdf" label="barplot from ${on_string}" /> 112 <data name="barplot" format="pdf" label="barplot from ${on_string}" />
106 </outputs> 113 </outputs>
107 <tests> 114 <tests>
108 <test> 115 <test>
116 <param name="input" value ="sample5.fa,sample4.fa,sample3.fa,sample2.fa,sample1.fa" ftype="fasta" />
117 <param name="genomeSource" value="history" />
118 <param name="ownFile" value ="2L-tail.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" />
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" />
123 <output_collection name="unmatched" type="list" count="5">
124 <element name="sample5.fa_unmatched" file="unmatched_5.fa" ftype="fasta"/>
125 <element name="sample4.fa_unmatched" file="unmatched_4.fa" ftype="fasta"/>
126 <element name="sample3.fa_unmatched" file="unmatched_3.fa" ftype="fasta"/>
127 <element name="sample2.fa_unmatched" file="unmatched_2.fa" ftype="fasta"/>
128 <element name="sample1.fa_unmatched" file="unmatched_1.fa" ftype="fasta"/>
129 </output_collection>
130 </test>
131 <test>
109 <param name="input" value ="sample1.fa" ftype="fasta" /> 132 <param name="input" value ="sample1.fa" ftype="fasta" />
110 <param name="genomeSource" value="history" /> 133 <param name="genomeSource" value="history" />
111 <param name="ownFile" value ="2L-tail.fa" ftype="fasta" /> 134 <param name="ownFile" value ="2L-tail.fa" ftype="fasta" />
112 <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" />
113 <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" />
114 <output name="output" ftype="tabular" file="sample1_output.tab" /> 137 <output name="output" ftype="tabular" file="sample1_output.tab" />
115 <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"/>
116 <output name="unmatched" ftype="fasta" file="unmatched_1.fa" /> 139 <output_collection name="unmatched" type="list">
140 <element name="sample1.fa_unmatched" file="unmatched_1.fa" ftype="fasta"/>
141 </output_collection>
117 </test> 142 </test>
118 <test> 143 <test>
119 <param name="input" value ="sample.fastq" ftype="fastq" /> 144 <param name="input" value ="sample.fastq" ftype="fastq" />
120 <param name="genomeSource" value="history" /> 145 <param name="genomeSource" value="history" />
121 <param name="ownFile" value ="2L-tail.fa" ftype="fasta" /> 146 <param name="ownFile" value ="2L-tail.fa" ftype="fasta" />
122 <param name="AdditionalQueries_0|ownFile" value="dme_miR21_hairpin.fa" ftype="fasta" /> 147 <param name="AdditionalQueries_0|ownFile" value="dme_miR21_hairpin.fa" ftype="fasta" />
123 <param name="AdditionalQueries_1|ownFile" value="Ensembl_transposon_set.fa" ftype="fasta" /> 148 <param name="AdditionalQueries_1|ownFile" value="Ensembl_transposon_set.fa" ftype="fasta" />
124 <output name="output" ftype="tabular" file="sample_output.tab" /> 149 <output name="output" ftype="tabular" file="sample_output.tab" />
125 <output name="barplot" ftype="pdf" file="sample_output.pdf" compare="sim_size" delta="500"/> 150 <output name="barplot" ftype="pdf" file="sample_output.pdf" compare="sim_size" delta="500"/>
126 <output name="unmatched" ftype="fasta" file="unmatched_2.fa" /> 151 <output_collection name="unmatched" type="list">
127 </test> 152 <element name="sample.fastq_unmatched" file="unmatched_fastq.fa" ftype="fasta"/>
128 <test> 153 </output_collection>
129 <param name="input" value ="sample5.fa,sample4.fa,sample3.fa,sample2.fa,sample1.fa" ftype="fasta" />
130 <param name="genomeSource" value="history" />
131 <param name="ownFile" value ="2L-tail.fa" ftype="fasta" />
132 <param name="AdditionalQueries_0|ownFile" value="dme_miR21_hairpin.fa" ftype="fasta" />
133 <param name="AdditionalQueries_1|ownFile" value="Ensembl_transposon_set.fa" ftype="fasta" />
134 <output name="output" ftype="tabular" file="multisample5_output.tab" />
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" />
137 </test> 154 </test>
138 </tests> 155 </tests>
139 <help> 156 <help>
140 157
141 **Introduction** 158 **Introduction**