diff draw_amr_matrix.xml @ 0:6044ca44e9f6 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/draw_amr_matrix.xml	Tue Feb 07 22:13:57 2023 +0000
@@ -0,0 +1,67 @@
+<tool id="draw_amr_matrix" name="PIMA: draw AMR matrix" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>of genes and drugs</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[
+#import re
+
+mkdir feature_hits_dir &&
+mkdir output_dir &&
+
+#for $i in $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' &&
+#end for
+
+python '$__tool_directory__/draw_amr_matrix.py'
+--amr_gene_drug '$amr_gene_drug'
+--feature_hits_dir '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 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>
+        </param>
+    </inputs>
+    <outputs>
+        <data name="process_log" format="txt" label="${tool.name} on ${on_string} (Process log)">
+            <filter>output_process_log == 'yes'</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="amr_gene_drug" value="amr_gene_drug.tsv" ftype="tsv"/>
+            <param name="feature_hits">
+                <collection type="list">
+                    <element name="amr_pima_md" value="amr_pima_md.bed"/>
+                </collection>
+            </param>
+            <output_collection name="amr_matrix_png" type="list" count="1">
+                <element name="amr_matrix" ftype="png">
+                    <assert_contents>
+                        <has_size value="38309" delta="500"/>
+                    </assert_contents>
+                </element>
+            </output_collection>
+        </test>
+    </tests>
+    <help>
+**What it does**
+
+Accepts a tabular AMR gene drugs file and a collection of best feature hits and draws an AMR matrix.
+    </help>
+    <expand macro="citations"/>
+</tool>
+