Mercurial > repos > greg > draw_amr_matrix
diff draw_amr_matrix.xml @ 2:9fcc1ffd7526 draft
Uploaded
author | greg |
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date | Fri, 10 Feb 2023 17:27:33 +0000 |
parents | 6044ca44e9f6 |
children | 33a0ea992043 |
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--- a/draw_amr_matrix.xml Fri Feb 10 17:27:13 2023 +0000 +++ b/draw_amr_matrix.xml Fri Feb 10 17:27:33 2023 +0000 @@ -7,26 +7,29 @@ <command detect_errors="exit_code"><![CDATA[ #import re -mkdir feature_hits_dir && +mkdir amr_feature_hits_dir && mkdir output_dir && -#for $i in $feature_hits: +#for $i in $amr_feature_hits: #set file_name = $i.file_name #set identifier = re.sub('[^\s\w\-\\.]', '_', str($i.element_identifier)) - ln -s '$file_name' 'feature_hits_dir/$identifier' && + ln -s '$file_name' 'amr_feature_hits_dir/$identifier' && #end for python '$__tool_directory__/draw_amr_matrix.py' ---amr_gene_drug '$amr_gene_drug' ---feature_hits_dir 'feature_hits_dir' +--amr_gene_drug_file '$amr_gene_drug_file' +--amr_deletions_file '$amr_deletions_file' +--amr_feature_hits_dir 'amr_feature_hits_dir' --output_dir 'output_dir' #if str($output_process_log) == 'yes': && mv 'process_log' '$process_log' #end if ]]></command> <inputs> - <param argument="--amr_gene_drug" type="data" format="tabular,tsv" label="Tabular AMR gene drugs file"/> - <param argument="--feature_hits" format="bed" type="data_collection" collection_type="list" label="Collection of feature hits BED files"/> + <param argument="--amr_feature_hits" format="bed" type="data_collection" collection_type="list" label="Collection of feature hits BED files"/> + <param argument="--amr_deletions_file" type="data" format="bed" optional="true" label="AMR deletions file" help="Optional, leave blank to ignore"/> + <param argument="--amr_mutations_file" type="data" format="tabular,tsv" optional="true" label="AMR mutations file" help="Optional, leave blank to ignore"/> + <param argument="--amr_gene_drug_file" type="data" format="tabular,tsv" label="AMR gene drugs file"/> <param name="output_process_log" type="select" display="radio" label="Output process log file?"> <option value="no" selected="true">No</option> <option value="yes">Yes</option> @@ -42,16 +45,16 @@ </outputs> <tests> <test> - <param name="amr_gene_drug" value="amr_gene_drug.tsv" ftype="tsv"/> - <param name="feature_hits"> + <param name="amr_feature_hits"> <collection type="list"> - <element name="amr_pima_md" value="amr_pima_md.bed"/> + <element name="amr_cds.bed" value="amr_cds.bed"/> </collection> </param> + <param name="amr_gene_drug_file" value="amr_gene_drug.tsv" ftype="tsv"/> <output_collection name="amr_matrix_png" type="list" count="1"> - <element name="amr_matrix" ftype="png"> + <element name="contig_1" ftype="png"> <assert_contents> - <has_size value="38309" delta="500"/> + <has_size value="25383" delta="100"/> </assert_contents> </element> </output_collection> @@ -60,7 +63,8 @@ <help> **What it does** -Accepts a tabular AMR gene drugs file and a collection of best feature hits and draws an AMR matrix. +Accepts a collection of best AMR feature hits, an optional AMR deletions BED file, an optional AMR mutations TSV file and a AMR gene +drug mappings file and draws an AMR matrix. </help> <expand macro="citations"/> </tool>