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comparison sr_bowtie_dataset_annotation.xml @ 4:e11f91575af6 draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
author artbio
date Wed, 20 Mar 2019 07:12:53 -0400
parents 008de522b3ea
children 279fdd92a615
comparison
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3:008de522b3ea 4:e11f91575af6
1 <tool id="sr_bowtie_dataset_annotation" name="Annotate smRNA dataset" version="2.1.0"> 1 <tool id="sr_bowtie_dataset_annotation" name="Annotate smRNA dataset" version="2.2.0">
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="1.1.2">bowtie</requirement> 4 <requirement type="package" version="1.1.2">bowtie</requirement>
5 <requirement type="package" version="1.3.2">r-optparse</requirement> 5 <requirement type="package" version="1.6.0">r-optparse</requirement>
6 <requirement type="package" version="2.2.1">r-ggplot2</requirement> 6 <requirement type="package" version="3.1.0">r-ggplot2</requirement>
7 <requirement type="package" version="0.4.1">r-scales</requirement> 7 <requirement type="package" version="0.8.0">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 -f $refGenomeSource1.ownFile genome 1>/dev/null &&
12 ln -s -f '$refGenomeSource1.ownFile' genome.fa &&
13 #set index_path = 'genome' 12 #set index_path = 'genome'
14 #else: 13 #else:
15 #set index_path = $refGenomeSource1.index.fields.path 14 #set index_path = $refGenomeSource1.index.fields.path
16 #end if 15 #end if
17 #if $input.is_of_type('fasta'): 16 #set method_prefix = "-v %s -k 1 --best" % str($mismatches)
17 #if $input[0].is_of_type('fasta'):
18 #set format = "-f" 18 #set format = "-f"
19 #elif $input.is_of_type('fastq'): 19 #elif $input[0].is_of_type('fastq'):
20 #set format = "-q" 20 #set format = "-q"
21 #end if 21 #end if
22 #if $format == '-f': 22
23 input_nbr_read=\$(( \$(wc -l < $input)/2)) && 23 #for $file in $input:
24 #elif $format == '-q': 24 #set sample=$file.element_identifier
25 input_nbr_read=\$(( \$(wc -l < $input)/4)) &&
26 #end if
27 #set method_prefix = "-v %s -k 1 --best" % str($mismatches)
28 bowtie -p \${GALAXY_SLOTS:-4}
29 $method_prefix
30 --al matched.fa
31 --un unmatched.fa
32 --suppress 6,7,8
33 $index_path $format '$input' > tabular_bowtie_output.tab &&
34 genome_aligned=\$(wc -l < matched.fa) &&
35 genome_aligned=\$(( \$genome_aligned/2)) &&
36 #if $refGenomeSource1.genomeSource == "history":
37 echo -e "$refGenomeSource1.ownFile.name\t\${genome_aligned}\n" > $output &&
38 #else:
39 echo -e "$refGenomeSource1.index.fields.dbkey\t\${genome_aligned}\n" > $output &&
40 #end if
41 #set counter = 0
42 #for $i in $AdditionalQueries:
43 rm -f genome.fa &&
44 #set $counter += 1
45 #if $counter != 1:
46 #set input = "class_unmatched.fa"
47 #else:
48 #set input = "matched.fa"
49 #end if
50 touch temp_class_matched.fa temp_class_unmatched.fa &&
51 bowtie-build -f $i.ownFile genome 1>/dev/null &&
52 ln -s -f '$i.ownFile' genome.fa &&
53 #set index_path = 'genome'
54 bowtie -p \${GALAXY_SLOTS:-4} 25 bowtie -p \${GALAXY_SLOTS:-4}
55 $method_prefix 26 $method_prefix
56 --al temp_class_matched.fa 27 --al matched.fa
57 --un temp_class_unmatched.fa 28 --un unmatched.fa
58 --suppress 6,7,8 29 --suppress 6,7,8
59 $index_path $format '$input' > tabular_bowtie_output.tab && 30 $index_path $format $file > tabular_bowtie_output.tab &&
60 class_aligned=\$(( \$(wc -l < temp_class_matched.fa)/2)) && 31 genome_aligned=\$(wc -l < matched.fa) &&
61 class_unaligned=\$(( \$(wc -l < temp_class_unmatched.fa)/2)) && 32 genome_aligned=\$(( \$genome_aligned/2)) &&
62 mv temp_class_unmatched.fa class_unmatched.fa && 33 #set counter = 0
63 echo -e "$i.ownFile.name\t\${class_aligned}\n" >> $output && 34 #for $i in $AdditionalQueries:
35 #set $counter += 1
36 #if $counter != 1:
37 #set to_align = "class_unmatched.fa"
38 #else:
39 #set to_align = "matched.fa"
40 #end if
41 bowtie-build -f $i.ownFile subgenome 1>/dev/null &&
42 touch tmp_class_matched.fa tmp_class_unmatched.fa &&
43 bowtie -p \${GALAXY_SLOTS:-4}
44 $method_prefix
45 --al tmp_class_matched.fa
46 --un tmp_class_unmatched.fa
47 --suppress 6,7,8
48 subgenome $format '$to_align' > tabular_bowtie_output.tab &&
49 class_aligned=\$(( \$(wc -l < tmp_class_matched.fa)/2)) &&
50 class_unaligned=\$(( \$(wc -l < tmp_class_unmatched.fa)/2)) &&
51 echo -e "$sample\t$i.ownFile.name\t\$class_aligned\t\${genome_aligned}" >> $output &&
52 mv tmp_class_unmatched.fa class_unmatched.fa &&
53 rm tmp_class_matched.fa &&
54 #end for
55 remaining=\$(( \$(wc -l < class_unmatched.fa)/2)) &&
56 echo -e "$sample\tNot classified\t\${remaining}\t\${genome_aligned}" >> $output &&
64 #end for 57 #end for
65 remaining=\$(( \$(wc -l < class_unmatched.fa)/2)) && 58
66 echo -e "Not classified\t\${remaining}\n" >> $output && 59
67 Rscript $__tool_directory__/barplot.r --input $output --barplot $barplot 60 Rscript $__tool_directory__/barplot.r --input $output --barplot $barplot
68 ]]></command> 61 ]]></command>
69 <inputs> 62 <inputs>
70 <param name="input" type="data" format="fasta,fastq" label="Input file: reads clipped from their adapter" help="Only with clipped, raw fasta or fastq files"/> 63 <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"/>
71 <param name="mismatches" type="select" label="Number of mismatches allowed" help="specify the number of mismatches allowed during alignments"> 64 <param name="mismatches" type="select" label="Number of mismatches allowed" help="specify the number of mismatches allowed during alignments">
72 <option value="0">0</option> 65 <option value="0">0</option>
73 <option value="1" selected="true">1</option> 66 <option value="1" selected="true">1</option>
74 <option value="2">2</option> 67 <option value="2">2</option>
75 <option value="3">3</option> 68 <option value="3">3</option>
97 <!-- End of other bowtie index selections --> 90 <!-- End of other bowtie index selections -->
98 </inputs> 91 </inputs>
99 <outputs> 92 <outputs>
100 <data format="tabular" name="output" label="Cascade Annotation Analysis"> 93 <data format="tabular" name="output" label="Cascade Annotation Analysis">
101 <actions> 94 <actions>
102 <action name="column_names" type="metadata" default="Reference Index,Number of reads" /> 95 <action name="column_names" type="metadata" default="Sample,Reference Index,Number of reads, Total reads" />
103 </actions> 96 </actions>
104 </data> 97 </data>
105 <data name="barplot" format="pdf" label="barplot from ${on_string}" /> 98 <data name="barplot" format="pdf" label="barplot from ${on_string}" />
106 </outputs> 99 </outputs>
107 <tests> 100 <tests>
110 <param name="genomeSource" value="history" /> 103 <param name="genomeSource" value="history" />
111 <param name="ownFile" value ="2L-tail.fa" ftype="fasta" /> 104 <param name="ownFile" value ="2L-tail.fa" ftype="fasta" />
112 <param name="AdditionalQueries_0|ownFile" value="dme_miR21_hairpin.fa" ftype="fasta" /> 105 <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" /> 106 <param name="AdditionalQueries_1|ownFile" value="Ensembl_transposon_set.fa" ftype="fasta" />
114 <output name="output" ftype="tabular" file="sample1_output.tab" /> 107 <output name="output" ftype="tabular" file="sample1_output.tab" />
115 <output name="barplot" ftype="pdf" file="sample1_output.pdf" /> 108 <output name="barplot" ftype="pdf" file="sample1_output.pdf" compare="sim_size" delta="500"/>
116 </test> 109 </test>
117 <test> 110 <test>
118 <param name="input" value ="sample.fastq" ftype="fastq" /> 111 <param name="input" value ="sample.fastq" ftype="fastq" />
119 <param name="genomeSource" value="history" /> 112 <param name="genomeSource" value="history" />
120 <param name="ownFile" value ="2L-tail.fa" ftype="fasta" /> 113 <param name="ownFile" value ="2L-tail.fa" ftype="fasta" />
121 <param name="AdditionalQueries_0|ownFile" value="dme_miR21_hairpin.fa" ftype="fasta" /> 114 <param name="AdditionalQueries_0|ownFile" value="dme_miR21_hairpin.fa" ftype="fasta" />
122 <param name="AdditionalQueries_1|ownFile" value="Ensembl_transposon_set.fa" ftype="fasta" /> 115 <param name="AdditionalQueries_1|ownFile" value="Ensembl_transposon_set.fa" ftype="fasta" />
123 <output name="output" ftype="tabular" file="sample_output.tab" /> 116 <output name="output" ftype="tabular" file="sample_output.tab" />
124 <output name="barplot" ftype="pdf" file="sample_output.pdf" /> 117 <output name="barplot" ftype="pdf" file="sample_output.pdf" compare="sim_size" delta="500"/>
118 </test>
119 <test>
120 <param name="input" value ="sample5.fa,sample4.fa,sample3.fa,sample2.fa,sample1.fa" ftype="fasta" />
121 <param name="genomeSource" value="history" />
122 <param name="ownFile" value ="2L-tail.fa" ftype="fasta" />
123 <param name="AdditionalQueries_0|ownFile" value="dme_miR21_hairpin.fa" ftype="fasta" />
124 <param name="AdditionalQueries_1|ownFile" value="Ensembl_transposon_set.fa" ftype="fasta" />
125 <output name="output" ftype="tabular" file="multisample5_output.tab" />
126 <output name="barplot" ftype="pdf" file="multisample5_output.pdf" compare="sim_size" delta="500" />
125 </test> 127 </test>
126 </tests> 128 </tests>
127 <help> 129 <help>
128 130
129 **Introduction** 131 **Introduction**