diff draw_amr_matrix.xml @ 4:33a0ea992043 draft

Uploaded

--- a/draw_amr_matrix.xml	Fri Feb 10 20:04:31 2023 +0000
+++ b/draw_amr_matrix.xml	Tue Feb 21 19:55:42 2023 +0000
@@ -8,8 +8,15 @@
 #import re
 
 mkdir amr_feature_hits_dir &&
+mkdir mutations_dir &&
 mkdir output_dir &&
 
+#if $reference_source.reference_source_selector == 'history':
+    ln -f -s '$reference_source.ref_file' reference.fa &&
+#else:
+    ln -f -s '$reference_source.ref_file.fields.path' reference.fa &&
+#end if
+
 #for $i in $amr_feature_hits:
     #set file_name = $i.file_name
     #set identifier = re.sub('[^\s\w\-\\.]', '_', str($i.element_identifier))
@@ -17,18 +24,47 @@
 #end for
 
 python '$__tool_directory__/draw_amr_matrix.py'
+--amr_feature_hits_dir 'amr_feature_hits_dir'
+#if str($amr_deletions_file) != 'None':
+    --amr_deletions_file '$amr_deletions_file'
+#end if
+#if str($amr_mutations_file) != 'None':
+    --amr_mutations_file '$amr_mutations_file'
+#end if
+#if str($amr_mutation_regions_file) != 'None':
+    --amr_mutation_regions_file '$amr_mutation_regions_file'
+    --region_mutations_output_file '$region_mutations_output_file'
+#end if
 --amr_gene_drug_file '$amr_gene_drug_file'
---amr_deletions_file '$amr_deletions_file'
---amr_feature_hits_dir 'amr_feature_hits_dir'
+--reference_genome reference.fa
+--mutations_dir 'mutations_dir'
 --output_dir 'output_dir'
 #if str($output_process_log) == 'yes':
     && mv 'process_log' '$process_log'
 #end if
 ]]></command>
     <inputs>
+        <conditional name="reference_source">
+            <param name="reference_source_selector" type="select" label="Select a reference genome from your history or use a cached genome index?">
+                <option value="cached">Use a cached genome index</option>
+                <option value="history">Select a genome from the history and build the index</option>
+            </param>
+            <when value="cached">
+                <param name="ref_file" type="select" label="Using reference genome" help="Select reference genome">
+                    <options from_data_table="all_fasta">
+                        <filter type="sort_by" column="2"/>
+                        <validator type="no_options" message="No reference genomes are available"/>
+                    </options>
+                </param>
+            </when>
+            <when value="history">
+                <param name="ref_file" type="data" format="fasta,fastq" label="Select the reference sequence" help="You can upload a FASTA file and use it as reference"/>
+            </when>
+        </conditional>
         <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_mutation_regions_file" type="data" format="bed" optional="true" label="AMR mutation regions BED 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>
@@ -36,18 +72,23 @@
         </param>
     </inputs>
     <outputs>
-        <data name="process_log" format="txt" label="${tool.name} on ${on_string} (Process log)">
+        <data name="process_log" format="txt" label="${tool.name} on ${on_string} (process log)">
             <filter>output_process_log == 'yes'</filter>
         </data>
+        <data name="region_mutations_output_file" format="tsv" label="${tool.name} on ${on_string} (region mutations)">
+            <filter>amr_mutation_regions_file not in [None, 'None']</filter>
+        </data>
         <collection name="amr_matrix_png" type="list" format="png">
             <discover_datasets pattern="(?P&lt;designation&gt;.+)\.(?P&lt;ext&gt;png)" directory="output_dir"/>
         </collection>
     </outputs>
     <tests>
         <test>
+            <param name="reference_source_selector" value="history"/>
+            <param name="ref_file" ftype="fasta" value="ref_genome.fasta"/>
             <param name="amr_feature_hits">
                 <collection type="list">
-                    <element name="amr_cds.bed" value="amr_cds.bed"/>
+                    <element name="amr_pima_md.bed" value="amr_pima_md.bed"/>
                 </collection>
             </param>
             <param name="amr_gene_drug_file" value="amr_gene_drug.tsv" ftype="tsv"/>