diff msmetaenhancer.xml @ 0:ce612a11b455 draft

"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 26bede767f65ec97ac84b8cc3309db0aced22d53"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/msmetaenhancer.xml	Tue Mar 22 15:33:37 2022 +0000
@@ -0,0 +1,80 @@
+<tool id="msmetaenhancer" name="MSMetaEnhancer" version="@TOOL_VERSION@+galaxy0">
+    <description>annotate MS data</description>
+
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="creator"/>
+
+    <requirements>
+        <requirement type="package" version="@TOOL_VERSION@">msmetaenhancer</requirement>
+    </requirements>
+
+    <command detect_errors="exit_code"><![CDATA[
+        sh ${msmetaenhancer_python_cli}
+    ]]> </command>
+
+    <configfiles>
+        <configfile name="msmetaenhancer_python_cli">
+            python3 ${__tool_directory__}/msmetaenhancer_wrapper.py \
+            --input_file "$input_file" \
+            --output_file "$output_file" \
+            #if $options.output_log:
+            --log_file "$log_file"\
+            #end if
+            #if len($ordered_jobs) != 0:
+                #set ordered_jobs = ",".join([str($job.ordered_jobs_select) for $job in $ordered_jobs]) + ","
+            #else:
+                #set ordered_jobs = ""
+            #end if
+            #if $jobs != 'None':
+                #set random_jobs = str($jobs)
+            #else:
+                #set random_jobs = ""
+            #end if
+            #set all_jobs = str($ordered_jobs) + str($random_jobs)
+            --jobs "$all_jobs"
+        </configfile>
+    </configfiles>
+
+    <inputs>
+        <param label="Input spectra dataset" name="input_file" type="data" format="msp" />
+
+        <repeat name="ordered_jobs" title="Ordered conversions">
+            <param name="ordered_jobs_select" type="select" label="Available conversions" multiple="false" optional="true">
+                <expand macro="job_options" />
+            </param>
+        </repeat>
+
+        <param name="jobs" type="select" label="Other conversions" multiple="true" optional="true">
+            <expand macro="job_options" />
+        </param>
+
+        <section name="options" title="Options">
+            <param label="Save the log file" name="output_log" type="boolean" truevalue="TRUE" falsevalue="FALSE"
+                   checked="false" help="Preserve a log with details about the annotation process."/>
+        </section>
+    </inputs>
+
+    <outputs>
+        <data label="MSMetaEnhancer on ${on_string}" name="output_file" format="msp" />
+        <data label="Log of MSMetaEnhancer on ${on_string}" name="log_file" format="txt">
+           <filter>options['output_log']</filter>
+       </data>
+    </outputs>
+
+    <tests>
+        <test>
+            <param name="input_file" value="sample.msp" ftype="msp" />
+            <param name="jobs" value="compound_name inchi PubChem,inchi canonical_smiles PubChem"/>
+            <output name="output_file" file="sample_out.msp" ftype="msp"/>
+        </test>
+    </tests>
+
+    <help>
+        <![CDATA[
+        @HELP@
+        ]]>
+    </help>
+
+</tool>