Mercurial > repos > galaxyp > openms_openswathmzmlfilecacher
changeset 6:691ae855ba41 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 981be1bde91d6d565693cd691553f77465e653bb
| author | galaxyp |
|---|---|
| date | Tue, 20 Mar 2018 14:42:35 -0400 |
| parents | e1c2ee148254 |
| children | b5121b003599 |
| files | readme.md test-data/FileFilter_1_input.mzML test-data/MetaProSIP_1_input.fasta test-data/MetaProSIP_1_input.featureXML test-data/MetaProSIP_1_input.mzML test-data/MetaProSIP_1_output_1.csv test-data/MetaProSIP_1_output_2.csv test-data/MzMLSplitter_output_part1.mzML test-data/MzMLSplitter_output_part2.mzML |
| diffstat | 9 files changed, 3546 insertions(+), 10 deletions(-) [+] |
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--- a/readme.md Mon Feb 12 12:56:52 2018 -0500 +++ b/readme.md Tue Mar 20 14:42:35 2018 -0400 @@ -170,16 +170,6 @@ </tests> ``` - - * `This section might not be up to date. It might be worth trying if these tools will run now.` These tools have multiple outputs (number of inputs = number of outputs) which is not yet supported in - by the automatic conversion step and are therefore in `tools_blacklist.txt`: - * SeedListGenerator - * SpecLibSearcher - * MapAlignerIdentification - * MapAlignerPoseClustering - * MapAlignerSpectrum - * MapAlignerRTTransformer - * Additionally cause of lacking dependencies, the following adapters have been removed in `SKIP_TOOLS_FILES.txt` as well: * OMSSAAdapter * MyrimatchAdapter
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/FileFilter_1_input.mzML Tue Mar 20 14:42:35 2018 -0400 @@ -0,0 +1,336 @@ +<?xml version="1.0" encoding="ISO-8859-1"?> +<mzML xmlns="http://psi.hupo.org/ms/mzml" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psi.hupo.org/ms/mzml http://psidev.info/files/ms/mzML/xsd/mzML1.1.0.xsd" accession="" version="1.1.0"> + <cvList count="2"> + <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" URI="http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo"/> + <cv id="UO" fullName="Unit Ontology" URI="http://obo.cvs.sourceforge.net/obo/obo/ontology/phenotype/unit.obo"/> + </cvList> + <fileDescription> + <fileContent> + <cvParam cvRef="MS" accession="MS:1000294" name="mass spectrum" /> + </fileContent> + <contact> + <cvParam cvRef="MS" accession="MS:1000586" name="contact name" value=", " /> + <cvParam cvRef="MS" 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/MetaProSIP_1_input.fasta Tue Mar 20 14:42:35 2018 -0400 @@ -0,0 +1,6 @@ +>contig23640_802236 length=2326 numreads=28 strand:-1 frame:0 orf_location:136:990 +GGIPNEENWNFGSSDGSGLPVRGSGQRRDVLGRLCRRNFTSSIGQSVNVRDVEASGFAGG +MSRYHFKYGGAVDPTVLGGVKLGTWFVKEGFAGWSGYPDWCKYFGFYTDFSYHRFYTRDN +RISGTDFFAAYGGGSAALGDVGFMKTEGMVATWAFMLAARYGFFQDSEVPFGRLQPYVAV +GPAIMFSSMKPKIWTQFNEPNVGFPNPDLVYSPGNQSSTDLGLAVDTGIRYMCLKNVSLD +ISFKYRYAQPHYNFSGQDGSVMVPAHMSLSPALNLYSFQAGVAYHF
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/MetaProSIP_1_input.featureXML Tue Mar 20 14:42:35 2018 -0400 @@ -0,0 +1,129 @@ +<?xml version="1.0" encoding="ISO-8859-1"?> +<featureMap version="1.9" xsi:noNamespaceSchemaLocation="http://open-ms.sourceforge.net/schemas/FeatureXML_1_9.xsd" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"> + <dataProcessing completion_time="2017-12-08T12:44:40"> + <software name="FileFilter" version="2.3.0" /> + <processingAction name="Data filtering" /> + <UserParam type="string" name="parameter: in" value="MetaProSIP_1_input.featureXML"/> + <UserParam type="string" name="parameter: in_type" value=""/> + <UserParam type="string" name="parameter: out" value="MetaProSIP_1_input.featureXML"/> + <UserParam type="string" name="parameter: out_type" value=""/> + <UserParam type="string" name="parameter: rt" value=":"/> + <UserParam type="string" name="parameter: mz" value=":"/> + <UserParam type="string" name="parameter: int" value=":"/> + <UserParam type="string" name="parameter: sort" value="false"/> + <UserParam type="string" name="parameter: log" value=""/> + <UserParam type="int" name="parameter: debug" value="0"/> + <UserParam type="int" name="parameter: threads" value="1"/> + <UserParam type="string" name="parameter: no_progress" value="false"/> + <UserParam type="string" name="parameter: force" value="false"/> + <UserParam type="string" name="parameter: test" value="false"/> + <UserParam type="float" name="parameter: peak_options:sn" value="0"/> + <UserParam type="intList" name="parameter: peak_options:rm_pc_charge" value="[]"/> + <UserParam type="string" name="parameter: peak_options:pc_mz_range" value=":"/> + <UserParam type="floatList" name="parameter: peak_options:pc_mz_list" value="[]"/> + <UserParam type="intList" name="parameter: peak_options:level" value="[1, 2, 3]"/> + <UserParam type="string" name="parameter: peak_options:sort_peaks" value="false"/> + <UserParam type="string" name="parameter: 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/MetaProSIP_1_output_2.csv Tue Mar 20 14:42:35 2018 -0400 @@ -0,0 +1,3 @@ +Peptide Sequence Feature Quality Report Spectrum Quality report scores Sample Name Protein Accessions Description Unique #Ambiguity members Score RT Exp. m/z Theo. m/z Charge TIC fraction #non-natural weights Peak intensities Group Global Peptide LR RIA 1 LR of RIA 1 INT 1 Cor. 1 RIA 2 LR of RIA 2 INT 2 Cor. 2 RIA 3 LR of RIA 3 INT 3 Cor. 3 RIA 4 LR of RIA 4 INT 4 Cor. 4 RIA 5 LR of RIA 5 INT 5 Cor. 5 RIA 6 LR of RIA 6 INT 6 Cor. 6 RIA 7 LR of RIA 7 INT 7 Cor. 7 RIA 8 LR of RIA 8 INT 8 Cor. 8 RIA 9 LR of RIA 9 INT 9 Cor. 9 RIA 10 LR of RIA 10 INT 10 Cor. 10 +YGGAVDPTVLGGVK feature test_mode_enabled.mzML CONTIG23640_802236 length=2326 numreads=28 strand:-1 frame:0 orf_location:136:990 1 1 0.174659044235501 80.52 666.8623 666.8615 2 0.831887919884232 7 659720 461384 165174 49177 14782 11728 6541 7410 10868 8404 9437 9556 10203 12619 12159 15831 16288 19847 19258 22222 21275 21576 21294 22006 24019 19046 17493 19060 17884 15631 15769 13964 14131 10090 9445 9216 7297 6670 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.269627132474428 0.6 1.0 1432378.6 1.0 36.5 0.0 146375.7 0.9 +
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