Mercurial > repos > artbio > sr_bowtie_dataset_annotation
comparison sr_bowtie_dataset_annotation.xml @ 9:6bf9de09aa74 draft
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit c8f13ba73552ccf7db7c22859b7fdc6ad121cdf0"
author | artbio |
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date | Mon, 11 Apr 2022 00:27:41 +0000 |
parents | 3519c2de7fac |
children | fd4a60fc3fca |
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8:3519c2de7fac | 9:6bf9de09aa74 |
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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** |