Mercurial > repos > galaxyp > openms_openswathconfidencescoring
changeset 6:6cad174923c0 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 981be1bde91d6d565693cd691553f77465e653bb
| author | galaxyp |
|---|---|
| date | Tue, 20 Mar 2018 14:56:42 -0400 |
| parents | 22f0e925d711 |
| children | b1cacc7586e2 |
| 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 13:02:17 2018 -0500 +++ b/readme.md Tue Mar 20 14:56:42 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
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/MetaProSIP_1_input.fasta Tue Mar 20 14:56:42 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 14:56:42 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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