diff qcxms_getres.xml @ 0:ef51824f6d04 draft

planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/qcxms commit 4018b84dd3c735d16f488094f001a19e634fe1a2

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qcxms_getres.xml	Fri Mar 08 10:55:44 2024 +0000
@@ -0,0 +1,75 @@
+<tool id="qcxms_getres" name="QCxMS get results" version="@TOOL_VERSION@+galaxy0" profile="22.09">
+    <description>Get result of the Production run to obtain a QCxMS simulated mass spectrum</description>
+    
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="edam"/>
+    <expand macro="creator"/>
+    <expand macro="requirements"/>
+
+    <command detect_errors="exit_code"><![CDATA[
+        python3 '${get_res}' &&
+        /plotms_bin/PlotMS.v.6.2.0/plotms &&
+        sh ${__tool_directory__}/msp_out.sh
+    ]]></command>
+
+    <configfiles>
+        <configfile name="get_res">
+#set res_collection = str("', '").join([str($f) for $f in $res_files])
+
+with open('$mol', 'r') as file:
+    lines = file.readlines()
+    molname = lines[1]
+
+with open('molname.txt', 'w') as file:
+    file.write(molname)
+
+input_files = '$res_collection'
+output_file = 'tmpqcxms.res'
+
+with open(output_file, 'w') as output:
+    for file_path in input_files:
+        with open(file_path, 'r') as input_file:
+            output.write(input_file.read())
+
+        </configfile>
+    </configfiles>
+
+    <inputs>
+        <param type="data" name="mol" label="Molecule 3D structure [.xzy]" format="xyz" />
+        <param type="data_collection" collection_type="list" name="res_files" label="res files [.res]" format="txt,text"/>
+    </inputs>
+
+    <outputs>
+        <data name="msp_output" format="msp" from_work_dir="simulated_spectra.msp" label="simulated_spectra.msp generated by ${tool.name} on ${on_string}"/>
+    </outputs>
+
+    <tests>
+        <test>
+            <param name="mol" value="mol.xyz" ftype="xyz"/>
+            <param name="res_files">
+                <collection type="list">
+                  <element name="res_files_1" value="res_files/TMP.1_qcxms.txt" />
+                  <element name="res_files_2" value="res_files/TMP.2_qcxms.txt" />
+                  <element name="res_files_3" value="res_files/TMP.3_qcxms.txt" />
+                </collection>
+            </param>
+            <output name="msp_output" file="output.msp" ftype="msp"/>
+        </test>
+    </tests>
+
+    <help><![CDATA[
+        The QCxMS getres tool is used to simulate mass spectra for a given molecule. 
+        This tool take res and molecules files and generates simulated mass spectra.
+        ]]>
+    </help>
+
+    <citations>
+        <citation type="doi">10.1002/anie.201300158</citation>
+        <citation type="doi">10.1039/C4OB01668H</citation>
+        <citation type="doi">10.1021/jp5096618</citation>
+        <citation type="doi">10.1255/ejms.1313</citation>
+        <citation type="doi">10.1021/acs.jpca.6b02907</citation>
+    </citations>
+</tool>