diff thermo_converter.xml @ 5:77a18a61aeed draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 2c29e2fadeba9be11e81420f24e7a6429ef52aa7"

--- a/thermo_converter.xml	Fri Apr 26 14:33:21 2019 -0400
+++ b/thermo_converter.xml	Fri Aug 30 10:28:22 2019 -0400
@@ -1,60 +1,193 @@
-<tool id="thermo_raw_file_converter" name="Thermo" version="1.1.2">
+<tool id="thermo_raw_file_converter" name="Thermo" version="1.1.10">
     <description>RAW file converter</description>
     <requirements>
-        <requirement type="package" version="1.1.2">ThermoRawFileParser</requirement>
+        <requirement type="package" version="1.1.10">ThermoRawFileParser</requirement>
     </requirements>
     <command>
 <![CDATA[
+#import re
 
-ln -s '$input' ./input.raw &&
+#set $temp_stderr = "thermo_converter_stderr"
+
+echo "" > $temp_stderr &&
 
-ThermoRawFileParser.sh
-    -i=input.raw
-    -o=./
+mkdir ./raws_folder &&
+mkdir ./output_folder &&
+#for $input_raw in $input:
+    #if len($input) > 1
+        #set $input_name = re.sub('[^\w\-\.]', '_',$input_raw.element_identifier.split('/')[-1].replace(".raw", "") + ".raw")
+        ln -s -f '${input_raw}' './raws_folder/${input_name}' &&
+    #else:
+        ln -s -f '${input_raw}' './raws_folder/input.raw' &&
+    #end if
+#end for
+
+(ThermoRawFileParser.sh
+    -d=./raws_folder
+    -o=./output_folder
     -f=$output_format
-    #if $metadata:
-        --metadata=1
+    #if $output_metadata_selector != "off":
+        --metadata="${output_metadata_selector}"
     #end if
+    $zlib_boolean
+    $peakpicking_boolean
+    $ignore_instrument_errors_boolean
+
+    2>> $temp_stderr)
+
     &&
-    #if $output_format == '0':
-        mv ./input.mgf '$output'
-    #else:
-        mv ./input.mzML '$output'
+
+    #if len($input) == 1:
+        #if $output_format == "0":
+            mv ./output_folder/input.mgf ./output_file.out &&
+        #else if $output_format == "1":
+            mv ./output_folder/input.mzML ./output_file.out &&
+        #else if $output_format == "2":
+            mv ./output_folder/input.mzML ./output_file.out &&
+        #end if
+
+        #if $output_metadata_selector != "off":
+            #if $output_metadata_selector == "0":
+                mv ./output_folder/input-metadata.json ./input-metadata.txt &&
+            #else if $output_metadata_selector == "1":
+                mv ./output_folder/input-metadata.txt ./input-metadata.txt &&
+            #end if
+        #end if
     #end if
+
+    cat $temp_stderr 2>&1;
 ]]>
     </command>
     <inputs>
-        <param name="input" type="data" format="thermo.raw" label="Thermo RAW file" help="" />
-        <param name="metadata" type="boolean" truevalue="" falsevalue="" checked="False"
-            label="Output metadata" help="" />
-        <param name="output_format" type="select" label="Choose an output format">
+        <param name="input" type="data" format="thermo.raw" label="Thermo RAW file" help="" multiple="true"
+          optional="False" />
+
+        <param name="output_format" type="select" label="Output format">
             <option value="0">mgf</option>
             <option value="1" selected="True">mzml</option>
+            <option value="2">Indexed mzml</option>
         </param>
+
+        <param name="zlib_boolean" type="boolean" truevalue="" falsevalue="-z" checked="true"
+            label="Use zlib compression for the m/z ratios and intensities" help="" />
+
+        <param name="peakpicking_boolean" type="boolean" truevalue="" falsevalue="-p" checked="true"
+            label="Use the peak picking provided by the native thermo library" help="" />
+
+        <param name="ignore_instrument_errors_boolean" type="boolean" truevalue="-e" falsevalue="" checked="true"
+            label="Ignore missing instrument properties" help="If false, it stops the conversion if instrument properties are missing" />
+
+        <param name="output_metadata_selector" type="select" label="Output metadata" >
+            <option value="off" selected="True">No</option>
+            <option value="0">json</option>
+            <option value="1">txt</option>
+        </param>
+
     </inputs>
     <outputs>
-        <data format="mzml" name="output" from_work_dir="input.mzML" label="${tool.name} on ${on_string}">
+
+        <!-- We use simple data outputs if we just have one file, for backwards compatibility -->
+
+        <data name="output" format="mzml" from_work_dir="output_file.out" label="${tool.name} on ${on_string}">
+            <filter>(str(input)).count(',') == 0</filter> <!-- funny way of counting the number of input files! -->
             <change_format>
                 <when input="output_format" value="0" format="mgf" />
+                <when input="output_format" value="2" format="txt" />
+            </change_format>
+        </data>
+
+        <data name="output_metadata" format="txt" label="${tool.name} on ${on_string}: Metadata" from_work_dir="input-metadata.txt">
+            <filter>str(output_metadata_selector) != "off"</filter>
+            <filter>(str(input)).count(',') == 0</filter>
+            <change_format>
+                <when input="output_metadata_selector" value="0" format="json" />
             </change_format>
         </data>
-        <data format="txt" name="output_metadata" from_work_dir="input-metadata.txt" label="${tool.name} on ${on_string}: Metadata">
-            <filter>metadata</filter>
-        </data>
+
+        <!-- We use collections if we have multiple input files -->
+
+        <collection name="output_mgf_collection" type="list" label="${tool.name} on ${on_string}: MGF">
+            <filter>output_format == "0"</filter>
+            <filter>(str(input)).count(',') > 0</filter>
+            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.mgf" directory="output_folder" ext="mgf"/>
+        </collection>
+
+        <collection name="output_mzml_collection" type="list" label="${tool.name} on ${on_string}: mzML">
+            <filter>output_format == "1"</filter>
+            <filter>(str(input)).count(',') > 0</filter>
+            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.mzML" ext="mzml" directory="output_folder"/>
+        </collection>
+
+        <collection name="output_indexedmzml_collection" type="list" label="${tool.name} on ${on_string}: Indexed mzML">
+            <filter>output_format == "2"</filter>
+            <filter>(str(input)).count(',') > 0</filter>
+            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.mzML" ext="mzml" directory="output_folder"/>
+        </collection>
+
+        <collection name="output_metadata_collection" type="list" label="${tool.name} on ${on_string}: metadata">
+            <filter>output_metadata_selector != "off"</filter>
+            <filter>(str(input)).count(',') > 0</filter>
+            <discover_datasets pattern="(?P&lt;designation&gt;.+)-metadata.txt" ext="txt" directory="output_folder"/>
+            <discover_datasets pattern="(?P&lt;designation&gt;.+)-metadata.json" ext="json" directory="output_folder"/>
+        </collection>
+
     </outputs>
+
     <tests>
-        <test>
-            <param name="input" value="fake_input.txt"/>
-            <assert_command>
-                <has_text text="ThermoRawFileParser.sh"/>
-            </assert_command>
+        <!-- Basic test -->
+        <test expect_num_outputs="1">
+            <param name="input" value="really_small.raw"/>
+            <param name="output_format" value="1"/>
+            <output name="output" file="really_small.mzml" ftype="mzml" compare="sim_size" delta="3000" />
         </test>
-        <test>
-            <param name="input" value="fake_input.txt"/>
+
+        <!-- Testing contents of converted mgf file with txt metadata -->
+        <test expect_num_outputs="2">
+            <param name="input" value="really_small.raw"/>
             <param name="output_format" value="0"/>
-            <assert_command>
-                <has_text text="-f=0"/>
-            </assert_command>
+            <param name="output_metadata_selector" value="1"/>
+            <output name="output">
+                <assert_contents>
+                    <has_text text="SCANS=36"/>
+                    <has_text text="RTINSECONDS=73.863181104"/>
+                    <has_text text="PEPMASS=675.248779296875"/>
+                    <has_text text="CHARGE=2+"/>
+                    <has_text text="121.3116455 920.2367553711"/>
+                    <has_text text="229.2241211 1137.6958007813"/>
+                    <has_text text="1577.8967285 1487.9519042969"/>
+                </assert_contents>
+            </output>
+            <output name="output_metadata" ftype="txt">
+                <assert_contents>
+                    <has_text text="Instrument model=[MS, MS:1000494, Thermo Scientific instrument model, Orbitrap Fusion]"/>
+                    <has_text text="Instrument name=Orbitrap Fusion"/>
+                    <has_text text="Instrument serial number=[MS, MS:1000529, instrument serial number, FSN10188]"/>
+                    <has_text text="Software version=[NCIT, NCIT:C111093, Software Version, 3.1.2412.17]"/>
+                    <has_text text="Mass resolution=[MS, MS:1000011, mass resolution, 0.500]"/>
+                    <has_text text="Number of scans=101"/>
+                    <has_text text="Scan range=1;101"/>
+                    <has_text text="Scan start time=[MS, MS:1000016, scan start time, 0.89]"/>
+                    <has_text text="Time range=0.89;1.59"/>
+                    <has_text text="Mass range=120.0000;2000.0000"/>
+                </assert_contents>
+            </output>
+
+        </test>
+
+        <!-- Basic mzml collection test -->
+        <test expect_num_outputs="1">
+            <param name="input" value="really_small.raw,really_small_2.raw"/>
+            <param name="output_format" value="1"/>
+            <output_collection name="output_mzml_collection" type="list" count="2"/>
+        </test>
+
+        <!-- mgf collection test with metadata -->
+        <test expect_num_outputs="2">
+            <param name="input" value="really_small.raw,really_small_2.raw,really_small_3.raw"/>
+            <param name="output_format" value="0"/>
+            <param name="output_metadata_selector" value="0"/>
+            <output_collection name="output_mgf_collection" type="list" count="3"/>
+            <output_collection name="output_metadata_collection" type="list" count="3"/>
         </test>
     </tests>
     <help>