Mercurial > repos > galaxyp > thermo_raw_file_converter
changeset 8:26c6706bfb07 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit a502d3fbf1f1ecfca1c9b115beab9d9c0e358fb5"
| author | galaxyp |
|---|---|
| date | Sat, 25 Jul 2020 16:26:42 -0400 |
| parents | 63769c4217a7 |
| children | 92ac8e086317 |
| files | thermo_converter.xml |
| diffstat | 1 files changed, 53 insertions(+), 92 deletions(-) [+] |
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--- a/thermo_converter.xml Mon May 04 08:00:32 2020 -0400 +++ b/thermo_converter.xml Sat Jul 25 16:26:42 2020 -0400 @@ -1,4 +1,4 @@ -<tool id="thermo_raw_file_converter" name="Thermo" version="1.2.3"> +<tool id="thermo_raw_file_converter" name="Thermo" version="1.2.3+galaxy0"> <description>RAW file converter</description> <requirements> <requirement type="package" version="1.2.3">thermorawfileparser</requirement> @@ -9,13 +9,9 @@ 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 +#for $input_raw in $input_files: + #set $input_name = re.sub('[^\w\-\.]', '_',$input_raw.element_identifier.split('/')[-1].replace(".raw", "") + ".raw") + ln -s -f '${input_raw}' './raws_folder/${input_name}' && #end for ThermoRawFileParser.sh @@ -29,27 +25,10 @@ $peakpicking_boolean $ignore_instrument_errors_boolean - #if len($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 $output_metadata_selector == "1": - && mv ./output_folder/input-metadata.txt ./input-metadata.txt - #end if - #end if - #end if ]]> </command> <inputs> - <param name="input" type="data" format="thermo.raw" label="Thermo RAW file" help="" multiple="true" + <param name="input_files" type="data" format="thermo.raw" label="Thermo RAW file" help="" multiple="true" optional="False" /> <param name="output_format" type="select" label="Output format"> @@ -76,47 +55,23 @@ </inputs> <outputs> - <!-- We use simple data outputs if we just have one file, for backwards compatibility --> - - <data name="output" format="mzml" from_work_dir="output_file.out" label="${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 ${on_string}: Metadata" from_work_dir="input-metadata.txt"> - <filter>str(output_metadata_selector) != "off"</filter> - <filter>(str(input)).count(',') == 0</filter> - <change_format> - <when input="output_metadata_selector" value="0" format="json" /> - </change_format> - </data> - - <!-- We use collections if we have multiple input files --> - - <collection name="output_mgf_collection" type="list" label="${tool.name} on ${on_string}: MGF"> + <collection name="output_mgf_collection" type="list" label="${tool.name} on ${on_string}: MGF collection"> <filter>output_format == "0"</filter> - <filter>(str(input)).count(',') > 0</filter> <discover_datasets pattern="(?P<designation>.+)\.mgf" directory="output_folder" ext="mgf"/> </collection> - <collection name="output_mzml_collection" type="list" label="${tool.name} on ${on_string}: mzML"> + <collection name="output_mzml_collection" type="list" label="${tool.name} on ${on_string}: mzML collection"> <filter>output_format == "1"</filter> - <filter>(str(input)).count(',') > 0</filter> <discover_datasets pattern="(?P<designation>.+)\.mzML" ext="mzml" directory="output_folder"/> </collection> - <collection name="output_indexedmzml_collection" type="list" label="${tool.name} on ${on_string}: Indexed mzML"> + <collection name="output_indexedmzml_collection" type="list" label="${tool.name} on ${on_string}: Indexed mzML collection"> <filter>output_format == "2"</filter> - <filter>(str(input)).count(',') > 0</filter> <discover_datasets pattern="(?P<designation>.+)\.mzML" ext="mzml" directory="output_folder"/> </collection> - <collection name="output_metadata_collection" type="list" label="${tool.name} on ${on_string}: metadata"> + <collection name="output_metadata_collection" type="list" label="${tool.name} on ${on_string}: metadata collection"> <filter>output_metadata_selector != "off"</filter> - <filter>(str(input)).count(',') > 0</filter> <discover_datasets pattern="(?P<designation>.+)-metadata.txt" ext="txt" directory="output_folder"/> <discover_datasets pattern="(?P<designation>.+)-metadata.json" ext="json" directory="output_folder"/> </collection> @@ -124,56 +79,62 @@ </outputs> <tests> - <!-- Basic test --> + <!-- Basic mgf test - 1 file --> <test expect_num_outputs="1"> - <param name="input" value="really_small.raw" ftype="thermo.raw"/> + <param name="input_files" value="really_small.raw" ftype="thermo.raw"/> + <param name="output_format" value="0"/> + <output_collection name="output_mgf_collection" type="list" count="1"/> + + <!--<output name="output" file="really_small.mzml" ftype="mzml" compare="sim_size" delta="3000" />--> + </test> + + + <!-- Basic mzml test - 2 files --> + <test expect_num_outputs="1"> + <param name="input_files" value="really_small.raw,really_small_2.raw" ftype="thermo.raw"/> <param name="output_format" value="1"/> - <output name="output" file="really_small.mzml" ftype="mzml" compare="sim_size" delta="3000" /> + <output_collection name="output_mzml_collection" type="list" count="2"/> </test> <!-- Testing contents of converted mgf file with txt metadata --> <test expect_num_outputs="2"> - <param name="input" value="really_small.raw" ftype="thermo.raw"/> + <param name="input_files" value="really_small.raw" ftype="thermo.raw"/> <param name="output_format" value="0"/> <param name="output_metadata_selector" value="1"/> - <output name="output" ftype="mgf"> - <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" ftype="thermo.raw"/> - <param name="output_format" value="1"/> - <output_collection name="output_mzml_collection" type="list" count="2"/> + <output_collection name="output_mgf_collection" type="list" count="1"> + <element name="really_small" ftype="mgf"> + <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> + </element> + </output_collection> + <output_collection name="output_metadata_collection" type="list"> + <element name="really_small" 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> + </element> + </output_collection> </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="input_files" 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"/>