Mercurial > repos > galaxyp > openms_nucleicacidsearchengine
changeset 5:a19e844b82ad draft default tip
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
| author | galaxyp |
|---|---|
| date | Fri, 14 Jun 2024 21:31:16 +0000 |
| parents | 92864c71ac6a |
| children | |
| files | NucleicAcidSearchEngine.xml fill_ctd_clargs.py generate-foo.sh get_tests.py macros.xml prepare_test_data_manual.sh readme.md test-data.sh |
| diffstat | 8 files changed, 808 insertions(+), 590 deletions(-) [+] |
line wrap: on
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--- a/NucleicAcidSearchEngine.xml Thu Dec 01 19:13:13 2022 +0000 +++ b/NucleicAcidSearchEngine.xml Fri Jun 14 21:31:16 2024 +0000 @@ -1,8 +1,7 @@ -<?xml version='1.0' encoding='UTF-8'?> <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.--> -<!--Proposed Tool Section: [Utilities]--> +<!--Proposed Tool Section: [RNA]--> <tool id="NucleicAcidSearchEngine" name="NucleicAcidSearchEngine" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> - <description>Annotate nucleic acid identifications to MS/MS spectra.</description> + <description>Annotate nucleic acid identifications to MS/MS spectra</description> <macros> <token name="@EXECUTABLE@">NucleicAcidSearchEngine</token> <import>macros.xml</import> @@ -15,14 +14,14 @@ ## Preprocessing mkdir in && -ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && +cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && #if $database: mkdir database && - ln -s '$database' 'database/${re.sub("[^\w\-_]", "_", $database.element_identifier)}.$gxy2omsext($database.ext)' && + cp '$database' 'database/${re.sub("[^\w\-_]", "_", $database.element_identifier)}.$gxy2omsext($database.ext)' && #end if #if $digest: mkdir digest && - ln -s '$digest' 'digest/${re.sub("[^\w\-_]", "_", $digest.element_identifier)}.$gxy2omsext($digest.ext)' && + cp '$digest' 'digest/${re.sub("[^\w\-_]", "_", $digest.element_identifier)}.$gxy2omsext($digest.ext)' && #end if mkdir out && #if "id_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') @@ -118,37 +117,37 @@ <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> </configfiles> <inputs> - <param argument="-in" type="data" format="mzml" optional="false" label="Input file: spectra" help=" select mzml data sets(s)"/> + <param argument="-in" type="data" format="mzml" label="Input file: spectra" help=" select mzml data sets(s)"/> <param argument="-database" type="data" format="fasta" optional="true" label="Input file: sequence database" help="Required unless 'digest' is set select fasta data sets(s)"/> <param argument="-digest" type="data" format="sqlite" optional="true" label="Input file: pre-digested sequence database" help="Can be used instead of 'database'. Sets all 'oligo:...' parameters select sqlite data sets(s)"/> <section name="precursor" title="Precursor (parent ion) options" help="" expanded="false"> - <param name="mass_tolerance" argument="-precursor:mass_tolerance" type="float" optional="true" value="10.0" label="Precursor mass tolerance (+/- around uncharged precursor mass)" help=""/> - <param name="mass_tolerance_unit" argument="-precursor:mass_tolerance_unit" type="select" optional="true" label="Unit of precursor mass tolerance" help=""> + <param name="mass_tolerance" argument="-precursor:mass_tolerance" type="float" value="10.0" label="Precursor mass tolerance (+/- around uncharged precursor mass)" help=""/> + <param name="mass_tolerance_unit" argument="-precursor:mass_tolerance_unit" type="select" label="Unit of precursor mass tolerance" help=""> <option value="Da">Da</option> <option value="ppm" selected="true">ppm</option> <expand macro="list_string_san" name="mass_tolerance_unit"/> </param> - <param name="min_charge" argument="-precursor:min_charge" type="integer" optional="true" value="-1" label="Minimum precursor charge to be considered" help=""/> - <param name="max_charge" argument="-precursor:max_charge" type="integer" optional="true" value="-20" label="Maximum precursor charge to be considered" help=""/> + <param name="min_charge" argument="-precursor:min_charge" type="integer" value="-1" label="Minimum precursor charge to be considered" help=""/> + <param name="max_charge" argument="-precursor:max_charge" type="integer" value="-20" label="Maximum precursor charge to be considered" help=""/> <param name="include_unknown_charge" argument="-precursor:include_unknown_charge" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Include MS2 spectra with unknown precursor charge - try to match them in any possible charge between 'min_charge' and 'max_charge', at the risk of a higher error rate" help=""/> <param name="use_avg_mass" argument="-precursor:use_avg_mass" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use average instead of monoisotopic precursor masses (appropriate for low-resolution instruments)" help=""/> <param name="use_adducts" argument="-precursor:use_adducts" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Consider possible salt adducts (see 'precursor:potential_adducts') when matching precursor masses" help=""/> - <param name="potential_adducts" argument="-precursor:potential_adducts" type="text" optional="true" value="Na:+" label="Adducts considered to explain mass differences" help="Format: 'Element:Charge(+/-)', i.e. the number of '+' or '-' indicates the charge, e.g. 'Ca:++' indicates +2. Only used if 'precursor:use_adducts' is set (space separated list, in order to allow for spaces in list items surround them by single quotes)"> + <param name="potential_adducts" argument="-precursor:potential_adducts" type="text" value="Na:+" label="Adducts considered to explain mass differences" help="Format: 'Element:Charge(+/-)', i.e. the number of '+' or '-' indicates the charge, e.g. 'Ca:++' indicates +2. Only used if 'precursor:use_adducts' is set (space separated list, in order to allow for spaces in list items surround them by single quotes)"> <expand macro="list_string_val" name="potential_adducts"/> <expand macro="list_string_san" name="potential_adducts"/> </param> - <param name="isotopes" argument="-precursor:isotopes" type="text" optional="true" value="0 1 2 3 4" label="Correct for mono-isotopic peak misassignments" help="E.g.: 1 = precursor may be misassigned to the first isotopic peak. Ignored if 'use_avg_mass' is set (space separated list, in order to allow for spaces in list items surround them by single quotes)"> + <param name="isotopes" argument="-precursor:isotopes" type="text" value="0 1 2 3 4" label="Correct for mono-isotopic peak misassignments" help="E.g.: 1 = precursor may be misassigned to the first isotopic peak. Ignored if 'use_avg_mass' is set (space separated list, in order to allow for spaces in list items surround them by single quotes)"> <expand macro="list_integer_valsan" name="isotopes"/> </param> </section> <section name="fragment" title="Fragment (Product Ion) Options" help="" expanded="false"> - <param name="mass_tolerance" argument="-fragment:mass_tolerance" type="float" optional="true" value="10.0" label="Fragment mass tolerance (+/- around fragment m/z)" help=""/> - <param name="mass_tolerance_unit" argument="-fragment:mass_tolerance_unit" type="select" optional="true" label="Unit of fragment mass tolerance" help=""> + <param name="mass_tolerance" argument="-fragment:mass_tolerance" type="float" value="10.0" label="Fragment mass tolerance (+/- around fragment m/z)" help=""/> + <param name="mass_tolerance_unit" argument="-fragment:mass_tolerance_unit" type="select" label="Unit of fragment mass tolerance" help=""> <option value="Da">Da</option> <option value="ppm" selected="true">ppm</option> <expand macro="list_string_san" name="mass_tolerance_unit"/> </param> - <param name="ions" argument="-fragment:ions" multiple="true" type="select" optional="true" label="Fragment ions to include in theoretical spectra" help=""> + <param name="ions" argument="-fragment:ions" type="select" multiple="true" optional="false" label="Fragment ions to include in theoretical spectra" help=""> <option value="a-B" selected="true">a-B</option> <option value="a" selected="true">a</option> <option value="b" selected="true">b</option> @@ -162,182 +161,337 @@ </param> </section> <section name="modifications" title="Modification options" help="" expanded="false"> - <param name="variable" argument="-modifications:variable" multiple="true" type="select" optional="true" label="Variable modifications" help=""> - <option value="m1Am">m1Am</option> - <option value="m1Gm">m1Gm</option> - <option value="m1Im">m1Im</option> - <option value="m1acp3Y">m1acp3Y</option> - <option value="m1A">m1A</option> - <option value="m1G">m1G</option> - <option value="m1I">m1I</option> - <option value="m1Y">m1Y</option> - <option value="m28A">m28A</option> - <option value="msms2i6A">msms2i6A</option> - <option value="ges2U">ges2U</option> + <param name="variable" argument="-modifications:variable" type="select" multiple="true" optional="true" label="Variable modifications" help=""> + <option value="io6A">io6A</option> + <option value="s2U">s2U</option> <option value="k2C">k2C</option> - <option value="m2A">m2A</option> - <option value="ms2ct6A">ms2ct6A</option> + <option value="m2Gm">m2Gm</option> + <option value="Ym">Ym</option> + <option value="f5Cm">f5Cm</option> + <option value="Qbase">Qbase</option> + <option value="ac4Cm">ac4Cm</option> + <option value="imG-14">imG-14</option> + <option value="cm5s2U">cm5s2U</option> + <option value="mnm5s2U">mnm5s2U</option> + <option value="m227G">m227G</option> + <option value="yW-58">yW-58</option> + <option value="I">I</option> + <option value="g6A">g6A</option> + <option value="nm5U">nm5U</option> + <option value="m7G">m7G</option> + <option value="s2Um">s2Um</option> + <option value="Y">Y</option> + <option value="hm5C">hm5C</option> + <option value="m5U">m5U</option> + <option value="preQ0">preQ0</option> + <option value="o2yW">o2yW</option> + <option value="m5Um">m5Um</option> + <option value="preQ1">preQ1</option> + <option value="m66Am">m66Am</option> + <option value="ac6A">ac6A</option> <option value="ms2io6A">ms2io6A</option> - <option value="ms2hn6A">ms2hn6A</option> - <option value="ms2i6A">ms2i6A</option> - <option value="ms2m6A">ms2m6A</option> - <option value="ms2t6A">ms2t6A</option> - <option value="se2U">se2U</option> - <option value="s2Um">s2Um</option> - <option value="s2C">s2C</option> - <option value="s2U">s2U</option> <option value="Am">Am</option> - <option value="Cm">Cm</option> - <option value="Gm">Gm</option> <option value="Im">Im</option> - <option value="Ym">Ym</option> - <option value="Um">Um</option> - <option value="mcmo5Um">mcmo5Um</option> - <option value="Ar(p)">Ar(p)</option> - <option value="Gr(p)">Gr(p)</option> - <option value="(pN)2'3'>p">(pN)2'3'>p</option> - <option value="hm5Cm">hm5Cm</option> - <option value="m3Um">m3Um</option> + <option value="mnm5U">mnm5U</option> + <option value="m22G">m22G</option> + <option value="t6A">t6A</option> + <option value="m8A">m8A</option> + <option value="m7GpppN">m7GpppN</option> + <option value="m27GpppN">m27GpppN</option> + <option value="m227GpppN">m227GpppN</option> + <option value="mpppN">mpppN</option> + <option value="m28A">m28A</option> <option value="acp3D">acp3D</option> <option value="acp3Y">acp3Y</option> - <option value="acp3U">acp3U</option> - <option value="m3C">m3C</option> + <option value="imG">imG</option> + <option value="D">D</option> + <option value="N">N</option> + <option value="C+">C+</option> + <option value="m27Gm">m27Gm</option> + <option value="ho5C">ho5C</option> + <option value="inm5U">inm5U</option> + <option value="inm5Um">inm5Um</option> + <option value="inm5s2U">inm5s2U</option> + <option value="pppN">pppN</option> + <option value="GpppN">GpppN</option> + <option value="CoApN">CoApN</option> + <option value="m44C">m44C</option> + <option value="acCoApN">acCoApN</option> + <option value="malonyl-CoApN">malonyl-CoApN</option> + <option value="succinyl-CoApN">succinyl-CoApN</option> + <option value="ppN">ppN</option> + <option value="NADpN">NADpN</option> + <option value="m6t6A">m6t6A</option> + <option value="OHyWy">OHyWy</option> + <option value="pG(pN)">pG(pN)</option> + <option value="ncm5s2U">ncm5s2U</option> + <option value="nchm5U">nchm5U</option> + <option value="mchm5Um">mchm5Um</option> + <option value="pN">pN</option> + <option value="ges2U">ges2U</option> + <option value="cmnm5ges2U">cmnm5ges2U</option> + <option value="mnm5ges2U">mnm5ges2U</option> + <option value="nm5ges2U">nm5ges2U</option> + <option value="m5D">m5D</option> + <option value="mmpN">mmpN</option> + <option value="mpN">mpN</option> + <option value="5'-OH-N">5'-OH-N</option> + <option value="N2'3'cp">N2'3'cp</option> + <option value="ct6A">ct6A</option> + <option value="hm6A">hm6A</option> + <option value="f6A">f6A</option> + <option value="cnm5U">cnm5U</option> + <option value="mcmo5Um">mcmo5Um</option> + <option value="m5C">m5C</option> + <option value="ms2ct6A">ms2ct6A</option> + <option value="ht6A">ht6A</option> + <option value="msms2i6A">msms2i6A</option> + <option value="hm5Cm">hm5Cm</option> + <option value="pY">pY</option> + <option value="pm5C">pm5C</option> + <option value="ps2U">ps2U</option> + <option value="hn6A">hn6A</option> + <option value="pD">pD</option> + <option value="pm2G">pm2G</option> + <option value="pm66A">pm66A</option> + <option value="pGm">pGm</option> + <option value="pm5U">pm5U</option> + <option value="pm22G">pm22G</option> + <option value="pm3U">pm3U</option> + <option value="m5Cm">m5Cm</option> + <option value="Ar(p)">Ar(p)</option> + <option value="pac4C">pac4C</option> + <option value="pCm">pCm</option> + <option value="pppG">pppG</option> + <option value="pm7G">pm7G</option> + <option value="pm1A">pm1A</option> + <option value="pUm">pUm</option> + <option value="pAm">pAm</option> + <option value="pm4Cm">pm4Cm</option> + <option value="pC2'3'cp">pC2'3'cp</option> + <option value="tm5U">tm5U</option> + <option value="pm6A">pm6A</option> + <option value="pyW">pyW</option> + <option value="pm1G">pm1G</option> + <option value="pA2'3'cp">pA2'3'cp</option> + <option value="ps4U">ps4U</option> + <option value="pI">pI</option> + <option value="ppG">ppG</option> + <option value="pm2A">pm2A</option> + <option value="m1G">m1G</option> + <option value="pmcm5s2U">pmcm5s2U</option> + <option value="cmnm5Um">cmnm5Um</option> + <option value="pse2U">pse2U</option> + <option value="pt6A">pt6A</option> + <option value="pf5C">pf5C</option> + <option value="pppA">pppA</option> + <option value="pG">pG</option> + <option value="pG2'3'cp">pG2'3'cp</option> + <option value="pms2i6A">pms2i6A</option> + <option value="pcmo5U">pcmo5U</option> + <option value="Xm">Xm</option> + <option value="pm44C">pm44C</option> + <option value="pi6A">pi6A</option> + <option value="phm5C">phm5C</option> + <option value="pU">pU</option> + <option value="pAr(p)">pAr(p)</option> + <option value="pac4Cm">pac4Cm</option> + <option value="pGp">pGp</option> + <option value="m1I">m1I</option> + <option value="pU2'3'cp">pU2'3'cp</option> + <option value="mcm5U">mcm5U</option> + <option value="Gm">Gm</option> + <option value="pm4C">pm4C</option> + <option value="ncm5Um">ncm5Um</option> + <option value="pm5Um">pm5Um</option> + <option value="pmnm5U">pmnm5U</option> + <option value="pm3C">pm3C</option> + <option value="m5s2U">m5s2U</option> + <option value="yW">yW</option> + <option value="pC">pC</option> + <option value="pm6t6A">pm6t6A</option> + <option value="f5C">f5C</option> + <option value="pAp">pAp</option> + <option value="m1Am">m1Am</option> + <option value="m1Im">m1Im</option> + <option value="ApppN">ApppN</option> + <option value="AppppN">AppppN</option> + <option value="ApppppN">ApppppN</option> + <option value="m6ApppN">m6ApppN</option> + <option value="m6AppppN">m6AppppN</option> + <option value="m6ApppppN">m6ApppppN</option> + <option value="m7GppppN">m7GppppN</option> + <option value="Gr(p)">Gr(p)</option> + <option value="pm1Am">pm1Am</option> + <option value="pm1Gm">pm1Gm</option> + <option value="pm1Im">pm1Im</option> + <option value="pm1acp3Y">pm1acp3Y</option> + <option value="pm1I">pm1I</option> + <option value="pm1Y">pm1Y</option> + <option value="pk2C">pk2C</option> + <option value="ps2C">ps2C</option> + <option value="pm3Y">pm3Y</option> + <option value="nm5s2U">nm5s2U</option> + <option value="pm5Cm">pm5Cm</option> + <option value="pmchm5U">pmchm5U</option> + <option value="pinm5Um">pinm5Um</option> + <option value="pinm5s2U">pinm5s2U</option> + <option value="pinm5U">pinm5U</option> + <option value="pnm5U">pnm5U</option> + <option value="pncm5U">pncm5U</option> + <option value="pchm5U">pchm5U</option> + <option value="pcmnm5U">pcmnm5U</option> + <option value="pcm5U">pcm5U</option> + <option value="m2G">m2G</option> + <option value="pho5U">pho5U</option> + <option value="pmcm5Um">pmcm5Um</option> + <option value="pmcm5U">pmcm5U</option> + <option value="pmo5U">pmo5U</option> + <option value="pm5D">pm5D</option> + <option value="pmimG">pmimG</option> + <option value="phm5Cm">phm5Cm</option> + <option value="pIm">pIm</option> + <option value="pYm">pYm</option> + <option value="pmcmo5Um">pmcmo5Um</option> + <option value="m2A">m2A</option> + <option value="pGr(p)">pGr(p)</option> + <option value="pm28A">pm28A</option> + <option value="pmsms2i6A">pmsms2i6A</option> + <option value="pges2U">pges2U</option> + <option value="pms2ct6A">pms2ct6A</option> + <option value="pms2io6A">pms2io6A</option> + <option value="pms2hn6A">pms2hn6A</option> + <option value="pms2m6A">pms2m6A</option> + <option value="pms2t6A">pms2t6A</option> + <option value="ps2Um">ps2Um</option> + <option value="pm3Um">pm3Um</option> + <option value="pacp3D">pacp3D</option> + <option value="pacp3U">pacp3U</option> + <option value="pimG-14">pimG-14</option> + <option value="pmchm5Um">pmchm5Um</option> + <option value="pnm5ges2U">pnm5ges2U</option> + <option value="pnm5se2U">pnm5se2U</option> + <option value="pnm5s2U">pnm5s2U</option> + <option value="pnchm5U">pnchm5U</option> + <option value="pncm5Um">pncm5Um</option> + <option value="m4Cm">m4Cm</option> + <option value="pncm5s2U">pncm5s2U</option> + <option value="pcm5s2U">pcm5s2U</option> + <option value="pcmnm5Um">pcmnm5Um</option> + <option value="pcmnm5ges2U">pcmnm5ges2U</option> + <option value="pcmnm5se2U">pcmnm5se2U</option> + <option value="pcmnm5s2U">pcmnm5s2U</option> + <option value="pcnm5U">pcnm5U</option> + <option value="pf5Cm">pf5Cm</option> + <option value="pho5C">pho5C</option> + <option value="pm5s2U">pm5s2U</option> + <option value="m27G">m27G</option> + <option value="m22Gm">m22Gm</option> + <option value="pmnm5ges2U">pmnm5ges2U</option> + <option value="pmnm5se2U">pmnm5se2U</option> + <option value="pmnm5s2U">pmnm5s2U</option> + <option value="ptm5s2U">ptm5s2U</option> + <option value="ptm5U">ptm5U</option> + <option value="pyW-86">pyW-86</option> + <option value="pyW-72">pyW-72</option> + <option value="pyW-58">pyW-58</option> + <option value="ppreQ1">ppreQ1</option> + <option value="ppreQ0">ppreQ0</option> + <option value="m66A">m66A</option> + <option value="pm8A">pm8A</option> + <option value="pC+">pC+</option> + <option value="pG+">pG+</option> + <option value="pct6A">pct6A</option> + <option value="poQ">poQ</option> + <option value="pgalQ">pgalQ</option> + <option value="pgluQ">pgluQ</option> + <option value="pht6A">pht6A</option> + <option value="pOHyW">pOHyW</option> + <option value="pimG2">pimG2</option> + <option value="gluQ">gluQ</option> + <option value="pmanQ">pmanQ</option> + <option value="pOHyWy">pOHyWy</option> + <option value="pm27Gm">pm27Gm</option> + <option value="pQ">pQ</option> + <option value="pOHyWx">pOHyWx</option> + <option value="pmcmo5U">pmcmo5U</option> + <option value="pimG">pimG</option> + <option value="pm44Cm">pm44Cm</option> + <option value="pm2Gm">pm2Gm</option> + <option value="pm22Gm">pm22Gm</option> + <option value="ncm5U">ncm5U</option> + <option value="pm6Am">pm6Am</option> + <option value="pm66Am">pm66Am</option> + <option value="pio6A">pio6A</option> + <option value="pac6A">pac6A</option> + <option value="pf6A">pf6A</option> + <option value="pg6A">pg6A</option> + <option value="phm6A">phm6A</option> + <option value="phn6A">phn6A</option> + <option value="cm5U">cm5U</option> + <option value="pm27G">pm27G</option> + <option value="pm227G">pm227G</option> + <option value="pA">pA</option> + <option value="cmnm5s2U">cmnm5s2U</option> + <option value="cmo5U">cmo5U</option> <option value="m3Y">m3Y</option> <option value="m3U">m3U</option> - <option value="imG-14">imG-14</option> - <option value="s4U">s4U</option> - <option value="m5Cm">m5Cm</option> - <option value="m5Um">m5Um</option> - <option value="mchm5Um">mchm5Um</option> - <option value="mchm5U">mchm5U</option> - <option value="inm5s2U">inm5s2U</option> - <option value="inm5Um">inm5Um</option> - <option value="inm5U">inm5U</option> - <option value="nm5ges2U">nm5ges2U</option> - <option value="nm5se2U">nm5se2U</option> - <option value="nm5s2U">nm5s2U</option> - <option value="nm5U">nm5U</option> - <option value="nchm5U">nchm5U</option> - <option value="ncm5s2U">ncm5s2U</option> - <option value="ncm5Um">ncm5Um</option> - <option value="ncm5U">ncm5U</option> - <option value="chm5U">chm5U</option> - <option value="cm5s2U">cm5s2U</option> - <option value="cmnm5ges2U">cmnm5ges2U</option> + <option value="ms2m6A">ms2m6A</option> + <option value="Um">Um</option> + <option value="ms2i6A">ms2i6A</option> + <option value="m3C">m3C</option> <option value="cmnm5se2U">cmnm5se2U</option> - <option value="cmnm5s2U">cmnm5s2U</option> - <option value="cmnm5Um">cmnm5Um</option> - <option value="cmnm5U">cmnm5U</option> - <option value="cm5U">cm5U</option> - <option value="cnm5U">cnm5U</option> - <option value="f5Cm">f5Cm</option> - <option value="f5C">f5C</option> - <option value="ho5C">ho5C</option> - <option value="hm5C">hm5C</option> + <option value="ms2t6A">ms2t6A</option> + <option value="i6A">i6A</option> + <option value="m3Um">m3Um</option> + <option value="mcmo5U">mcmo5U</option> + <option value="mimG">mimG</option> + <option value="oQ">oQ</option> + <option value="preQ1base">preQ1base</option> + <option value="nm5se2U">nm5se2U</option> + <option value="m1Gm">m1Gm</option> <option value="ho5U">ho5U</option> + <option value="Q">Q</option> + <option value="xG">xG</option> <option value="mcm5s2U">mcm5s2U</option> - <option value="mcm5Um">mcm5Um</option> - <option value="mcm5U">mcm5U</option> + <option value="m44Cm">m44Cm</option> + <option value="s4U">s4U</option> + <option value="xC">xC</option> + <option value="yW-86">yW-86</option> + <option value="xA">xA</option> + <option value="chm5U">chm5U</option> <option value="mo5U">mo5U</option> - <option value="m5s2U">m5s2U</option> - <option value="mnm5ges2U">mnm5ges2U</option> - <option value="mnm5se2U">mnm5se2U</option> - <option value="mnm5s2U">mnm5s2U</option> - <option value="mnm5U">mnm5U</option> - <option value="m5C">m5C</option> - <option value="m5D">m5D</option> - <option value="m5U">m5U</option> - <option value="tm5s2U">tm5s2U</option> - <option value="tm5U">tm5U</option> - <option value="CoA(pN)">CoA(pN)</option> - <option value="acCoA(pN)">acCoA(pN)</option> - <option value="malonyl-CoA(pN)">malonyl-CoA(pN)</option> - <option value="succinyl-CoA(pN)">succinyl-CoA(pN)</option> - <option value="p(pN)">p(pN)</option> - <option value="5'-OH-N">5'-OH-N</option> - <option value="(pN)">(pN)</option> - <option value="NAD(pN)">NAD(pN)</option> - <option value="pp(pN)">pp(pN)</option> - <option value="yW-86">yW-86</option> + <option value="acp3U">acp3U</option> + <option value="xU">xU</option> <option value="yW-72">yW-72</option> - <option value="yW-58">yW-58</option> - <option value="preQ1tRNA">preQ1tRNA</option> - <option value="preQ0tRNA">preQ0tRNA</option> - <option value="m7G">m7G</option> - <option value="m7Gpp(pN)">m7Gpp(pN)</option> - <option value="m8A">m8A</option> - <option value="m2Gm">m2Gm</option> - <option value="m27Gm">m27Gm</option> - <option value="m27G">m27G</option> - <option value="m27Gpp(pN)">m27Gpp(pN)</option> - <option value="m22Gm">m22Gm</option> - <option value="m227G">m227G</option> - <option value="m227Gpp(pN)">m227Gpp(pN)</option> - <option value="m22G">m22G</option> - <option value="m2G">m2G</option> - <option value="m4Cm">m4Cm</option> - <option value="m44Cm">m44Cm</option> - <option value="m44C">m44C</option> - <option value="ac4Cm">ac4Cm</option> + <option value="mnm5se2U">mnm5se2U</option> + <option value="ms2hn6A">ms2hn6A</option> + <option value="m1acp3Y">m1acp3Y</option> + <option value="mcm5Um">mcm5Um</option> <option value="ac4C">ac4C</option> + <option value="m6Am">m6Am</option> + <option value="m1A">m1A</option> + <option value="Cm">Cm</option> + <option value="mchm5U">mchm5U</option> + <option value="galQ">galQ</option> + <option value="cmnm5U">cmnm5U</option> + <option value="m1Y">m1Y</option> + <option value="imG2">imG2</option> <option value="m4C">m4C</option> - <option value="m6Am">m6Am</option> - <option value="m66Am">m66Am</option> - <option value="m66A">m66A</option> - <option value="io6A">io6A</option> - <option value="ac6A">ac6A</option> - <option value="f6A">f6A</option> - <option value="g6A">g6A</option> - <option value="hm6A">hm6A</option> - <option value="hn6A">hn6A</option> - <option value="i6A">i6A</option> - <option value="m6t6A">m6t6A</option> + <option value="manQ">manQ</option> + <option value="tm5s2U">tm5s2U</option> + <option value="s2C">s2C</option> + <option value="OHyWx">OHyWx</option> + <option value="se2U">se2U</option> + <option value="preQ0base">preQ0base</option> <option value="m6A">m6A</option> - <option value="t6A">t6A</option> - <option value="Qbase">Qbase</option> - <option value="C+">C+</option> - <option value="mm(pN)">mm(pN)</option> - <option value="m(pN)">m(pN)</option> + <option value="OHyW">OHyW</option> + <option value="xX">xX</option> <option value="G+">G+</option> - <option value="ct6A">ct6A</option> - <option value="D">D</option> - <option value="oQ">oQ</option> - <option value="galQ">galQ</option> - <option value="mpp(pN)">mpp(pN)</option> - <option value="gluQ">gluQ</option> - <option value="pG(pN)">pG(pN)</option> - <option value="Gpp(pN)">Gpp(pN)</option> - <option value="ht6A">ht6A</option> - <option value="OHyW">OHyW</option> - <option value="I">I</option> - <option value="imG2">imG2</option> - <option value="manQ">manQ</option> - <option value="OHyWy">OHyWy</option> - <option value="mimG">mimG</option> - <option value="o2yW">o2yW</option> - <option value="preQ0base">preQ0base</option> - <option value="preQ1base">preQ1base</option> - <option value="Y">Y</option> - <option value="Q">Q</option> - <option value="OHyWx">OHyWx</option> - <option value="Xm">Xm</option> - <option value="xX">xX</option> - <option value="xA">xA</option> - <option value="xC">xC</option> - <option value="xG">xG</option> - <option value="xU">xU</option> - <option value="N">N</option> - <option value="cmo5U">cmo5U</option> - <option value="mcmo5U">mcmo5U</option> - <option value="yW">yW</option> - <option value="imG">imG</option> - <option value="dA">dA</option> - <option value="dC">dC</option> - <option value="dG">dG</option> - <option value="dU">dU</option> - <option value="dT">dT</option> <option value="3'-p">3'-p</option> <option value="5'-p">5'-p</option> + <option value="5'-p*">5'-p*</option> + <option value="3'-c">3'-c</option> <option value="mA">mA</option> <option value="mC">mC</option> <option value="mG">mG</option> @@ -365,43 +519,57 @@ <option value="mmmG?">mmmG?</option> <option value="ac4C/f5Cm?">ac4C/f5Cm?</option> <option value="acp3U/cmnm5Um?">acp3U/cmnm5Um?</option> + <option value="dA">dA</option> + <option value="dC">dC</option> + <option value="dG">dG</option> + <option value="dU">dU</option> + <option value="dT">dT</option> + <option value="A*">A*</option> + <option value="C*">C*</option> + <option value="G*">G*</option> + <option value="U*">U*</option> + <option value="dA*">dA*</option> + <option value="dC*">dC*</option> + <option value="dG*">dG*</option> + <option value="dU*">dU*</option> + <option value="dT*">dT*</option> <expand macro="list_string_san" name="variable"/> </param> - <param name="variable_max_per_oligo" argument="-modifications:variable_max_per_oligo" type="integer" optional="true" value="2" label="Maximum number of residues carrying a variable modification per candidate oligonucleotide" help=""/> + <param name="variable_max_per_oligo" argument="-modifications:variable_max_per_oligo" type="integer" value="2" label="Maximum number of residues carrying a variable modification per candidate oligonucleotide" help=""/> <param name="resolve_ambiguities" argument="-modifications:resolve_ambiguities" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Attempt to resolve ambiguous modifications" help="(e.g. 'mA?' for 'mA'/'Am') based on a-B ions.. This incurs a performance cost because two modifications have to be considered for each case.. Requires a-B ions to be enabled in parameter 'fragment:ions'"/> </section> <section name="oligo" title="Oligonucleotide (digestion) options (ignored if 'digest' input is used)" help="" expanded="false"> - <param name="min_size" argument="-oligo:min_size" type="integer" optional="true" value="5" label="Minimum size an oligonucleotide must have after digestion to be considered in the search" help=""/> - <param name="max_size" argument="-oligo:max_size" type="integer" optional="true" value="0" label="Maximum size an oligonucleotide must have after digestion to be considered in the search, leave at 0 for no limit" help=""/> - <param name="missed_cleavages" argument="-oligo:missed_cleavages" type="integer" optional="true" value="1" label="Number of missed cleavages" help=""/> - <param name="enzyme" argument="-oligo:enzyme" type="select" optional="true" label="The enzyme used for RNA digestion" help=""> - <option value="RNase_T1">RNase_T1</option> - <option value="cusativin">cusativin</option> + <param name="min_size" argument="-oligo:min_size" type="integer" value="5" label="Minimum size an oligonucleotide must have after digestion to be considered in the search" help=""/> + <param name="max_size" argument="-oligo:max_size" type="integer" value="0" label="Maximum size an oligonucleotide must have after digestion to be considered in the search, leave at 0 for no limit" help=""/> + <param name="missed_cleavages" argument="-oligo:missed_cleavages" type="integer" value="1" label="Number of missed cleavages" help=""/> + <param name="enzyme" argument="-oligo:enzyme" type="select" label="The enzyme used for RNA digestion" help=""> + <option value="RNase_A">RNase_A</option> + <option value="RNase_MC1">RNase_MC1</option> <option value="RNase_H">RNase_H</option> <option value="mazF">mazF</option> + <option value="cusativin">cusativin</option> + <option value="RNase_T1">RNase_T1</option> <option value="colicin_E5">colicin_E5</option> <option value="no cleavage" selected="true">no cleavage</option> + <option value="unspecific cleavage">unspecific cleavage</option> <option value="RNase_U2">RNase_U2</option> - <option value="RNase_A">RNase_A</option> - <option value="RNase_MC1">RNase_MC1</option> - <option value="unspecific cleavage">unspecific cleavage</option> <expand macro="list_string_san" name="enzyme"/> </param> </section> <section name="report" title="Reporting Options" help="" expanded="false"> - <param name="top_hits" argument="-report:top_hits" type="integer" optional="true" min="0" value="1" label="Maximum number of top-scoring hits per spectrum that are reported ('0' for all hits)" help=""/> + <param name="top_hits" argument="-report:top_hits" type="integer" min="0" value="1" label="Maximum number of top-scoring hits per spectrum that are reported ('0' for all hits)" help=""/> </section> <section name="fdr" title="False Discovery Rate options" help="" expanded="false"> <param name="decoy_pattern" argument="-fdr:decoy_pattern" type="text" optional="true" value="" label="String used as part of the accession to annotate decoy sequences" help="(e.g. 'DECOY_'). Leave empty to skip the FDR/q-value calculation"> <expand macro="list_string_san" name="decoy_pattern"/> </param> - <param name="cutoff" argument="-fdr:cutoff" type="float" optional="true" min="0.0" max="1.0" value="1.0" label="Cut-off for FDR filtering; search hits with higher q-values will be removed" help=""/> + <param name="cutoff" argument="-fdr:cutoff" type="float" min="0.0" max="1.0" value="1.0" label="Cut-off for FDR filtering; search hits with higher q-values will be removed" help=""/> <param name="remove_decoys" argument="-fdr:remove_decoys" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Do not score hits to decoy sequences and remove them when filtering" help=""/> </section> <expand macro="adv_opts_macro"> <param argument="-decharge_ms2" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Decharge the MS2 spectra for scoring" help=""/> <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> - <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> + <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true"> <expand macro="list_string_san" name="test"/> </param> </expand> @@ -439,7 +607,8 @@ <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> </data> </outputs> - <tests><!-- UTILS_NucleicAcidSearchEngine_1 --> + <tests> + <!-- TOPP_NucleicAcidSearchEngine_1 --> <test expect_num_outputs="5"> <section name="adv_opts"> <param name="decharge_ms2" value="false"/> @@ -448,10 +617,10 @@ </section> <param name="in" value="NucleicAcidSearchEngine_1.mzML"/> <param name="database" value="NucleicAcidSearchEngine_1.fasta"/> - <output name="out" file="NucleicAcidSearchEngine_12_out.mzTab" compare="sim_size" delta_frac="0.7" ftype="mztab"/> - <output name="id_out" file="NucleicAcidSearchEngine_11_out.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/> - <output name="db_out" file="NucleicAcidSearchEngine_13_out.tmp" compare="sim_size" delta_frac="0.7" ftype="sqlite"/> - <output name="digest_out" file="NucleicAcidSearchEngine_1_digest.oms" compare="sim_size" delta_frac="0.7" ftype="sqlite"/> + <output name="out" value="NucleicAcidSearchEngine_12_out.mzTab" compare="sim_size" delta_frac="0.7" ftype="mztab"/> + <output name="id_out" value="NucleicAcidSearchEngine_11_out.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/> + <output name="db_out" value="NucleicAcidSearchEngine_13_out.tmp" compare="sim_size" delta_frac="0.7" ftype="sqlite"/> + <output name="digest_out" value="NucleicAcidSearchEngine_1_digest.oms" compare="sim_size" delta_frac="0.7" ftype="sqlite"/> <section name="precursor"> <param name="mass_tolerance" value="5.0"/> <param name="mass_tolerance_unit" value="ppm"/> @@ -459,7 +628,7 @@ <param name="max_charge" value="-14"/> <param name="include_unknown_charge" value="true"/> <param name="use_avg_mass" value="false"/> - <param name="use_adducts" value="false"/> + <param name="use_adducts" value="true"/> <param name="potential_adducts" value=""K:+" "Na:+" "Na2:++" "K2:++" "NaK:++" "K3:+++" "Na3:+++" "NaK2:+++" "Na2K:+++""/> <param name="isotopes" value="0 1 2"/> </section> @@ -469,7 +638,6 @@ <param name="ions" value="a-B,c,w,y"/> </section> <section name="modifications"> - <param name="variable"/> <param name="variable_max_per_oligo" value="2"/> <param name="resolve_ambiguities" value="false"/> </section> @@ -493,8 +661,11 @@ <is_valid_xml/> </assert_contents> </output> + <assert_stdout> + <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> + </assert_stdout> </test> - <!-- UTILS_NucleicAcidSearchEngine_2 --> + <!-- TOPP_NucleicAcidSearchEngine_2 --> <test expect_num_outputs="4"> <section name="adv_opts"> <param name="decharge_ms2" value="false"/> @@ -503,9 +674,9 @@ </section> <param name="in" value="NucleicAcidSearchEngine_1.mzML"/> <param name="digest" value="NucleicAcidSearchEngine_1_digest.oms"/> - <output name="out" file="NucleicAcidSearchEngine_12_out.mzTab" compare="sim_size" delta_frac="0.7" ftype="mztab"/> - <output name="id_out" file="NucleicAcidSearchEngine_11_out.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/> - <output name="db_out" file="NucleicAcidSearchEngine_23_out.tmp" compare="sim_size" delta_frac="0.7" ftype="sqlite"/> + <output name="out" value="NucleicAcidSearchEngine_12_out.mzTab" compare="sim_size" delta_frac="0.7" ftype="mztab"/> + <output name="id_out" value="NucleicAcidSearchEngine_11_out.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/> + <output name="db_out" value="NucleicAcidSearchEngine_23_out.tmp" compare="sim_size" delta_frac="0.7" ftype="sqlite"/> <section name="precursor"> <param name="mass_tolerance" value="5.0"/> <param name="mass_tolerance_unit" value="ppm"/> @@ -513,7 +684,7 @@ <param name="max_charge" value="-14"/> <param name="include_unknown_charge" value="true"/> <param name="use_avg_mass" value="false"/> - <param name="use_adducts" value="false"/> + <param name="use_adducts" value="true"/> <param name="potential_adducts" value=""K:+" "Na:+" "Na2:++" "K2:++" "NaK:++" "K3:+++" "Na3:+++" "NaK2:+++" "Na2K:+++""/> <param name="isotopes" value="0 1 2"/> </section> @@ -523,7 +694,6 @@ <param name="ions" value="a-B,c,w,y"/> </section> <section name="modifications"> - <param name="variable"/> <param name="variable_max_per_oligo" value="2"/> <param name="resolve_ambiguities" value="false"/> </section> @@ -547,11 +717,14 @@ <is_valid_xml/> </assert_contents> </output> + <assert_stdout> + <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> + </assert_stdout> </test> </tests> <help><![CDATA[Annotate nucleic acid identifications to MS/MS spectra. -For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_NucleicAcidSearchEngine.html]]></help> +For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_NucleicAcidSearchEngine.html]]></help> <expand macro="references"/> </tool>
--- a/fill_ctd_clargs.py Thu Dec 01 19:13:13 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,70 +0,0 @@ -#!/usr/bin/env python3 - -import operator -from argparse import ArgumentParser -from functools import reduce # forward compatibility for Python 3 -from io import StringIO - -from CTDopts.CTDopts import ( - _Null, - CTDModel, - ModelTypeError, - Parameters -) - - -def getFromDict(dataDict, mapList): - return reduce(operator.getitem, mapList, dataDict) - - -def setInDict(dataDict, mapList, value): - getFromDict(dataDict, mapList[:-1])[mapList[-1]] = value - - -if __name__ == "__main__": - # note add_help=False since otherwise arguments starting with -h will - # trigger an error (despite allow_abbreviate) - parser = ArgumentParser(prog="fill_ctd_clargs", - description="fill command line arguments" - "into a CTD file and write the CTD file to stdout", - add_help=False, allow_abbrev=False) - parser.add_argument("--ini_file", dest="ini_file", help="input ini file", - metavar='INI', default=None, required=True) - parser.add_argument("--ctd_file", dest="ctd_file", help="input ctd file" - "if given then optional parameters from the ini file" - "will be filled with the defaults from this CTD file", - metavar='CTD', default=None, required=False) - args, cliargs = parser.parse_known_args() - - # load CTDModel - ini_model = None - try: - ini_model = CTDModel(from_file=args.ini_file) - except ModelTypeError: - pass - try: - ini_model = Parameters(from_file=args.ini_file) - except ModelTypeError: - pass - assert ini_model is not None, "Could not parse %s, seems to be no CTD/PARAMS" % (args.ini_file) - - # get a dictionary of the ctd arguments where the values of the parameters - # given on the command line are overwritten - ini_values = ini_model.parse_cl_args(cl_args=cliargs, ignore_required=True) - - if args.ctd_file: - ctd_model = CTDModel(from_file=args.ctd_file) - ctd_values = ctd_model.get_defaults() - for param in ini_model.get_parameters(): - if not param.required and (param.default is None or type(param.default) is _Null): - lineage = param.get_lineage(name_only=True) - try: - default = getFromDict(ctd_values, lineage) - except KeyError: - continue - setInDict(ini_values, lineage, default) - - # write the ctd with the values taken from the dictionary - out = StringIO() - ctd_tree = ini_model.write_ctd(out, ini_values) - print(out.getvalue())
--- a/generate-foo.sh Thu Dec 01 19:13:13 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,215 +0,0 @@ -#!/usr/bin/env bash - -# parse test definitions from OpenMS sources for a tool with a given id -function get_tests2 { - id=$1 - >&2 echo "generate tests for $id" - echo '<xml name="autotest_'"$id"'">' - - # get the tests from the CMakeLists.txt - # 1st remove some tests - # - OpenSwathMzMLFileCacher with -convert_back argument https://github.com/OpenMS/OpenMS/issues/4399 - # - IDRipper PATH gets empty causing problems. TODO But overall the option needs to be handled differentlt - # - several tools with duplicated input (leads to conflict when linking) - # - MaRaCluster with -consensus_out (parameter blacklister: https://github.com/OpenMS/OpenMS/issues/4456) - # - FileMerger with mixed dta dta2d input (ftype can not be specified in the test, dta can not be sniffed) - # - some input files are originally in a subdir (degenerated cases/), but not in test-data - # - OpenSwathAnalyzer 9/10: cachedMzML (not supported yet) - # - SiriusAdapter_4 depends on online service which may timeout .. so keep disabled https://github.com/OpenMS/OpenMS/pull/5010 - # - SiriusAdapter_10 should work in >2.8 https://github.com/OpenMS/OpenMS/issues/5869 - CMAKE=$(cat $OPENMSGIT/src/tests/topp/CMakeLists.txt $OPENMSGIT/src/tests/topp/THIRDPARTY/third_party_tests.cmake | - sed 's@${DATA_DIR_SHARE}/@@g' | - grep -v 'OpenSwathMzMLFileCacher .*-convert_back' | - sed 's/${TMP_RIP_PATH}/""/' | - grep -v "MaRaClusterAdapter.*-consensus_out"| - grep -v "FileMerger_1_input1.dta2d.*FileMerger_1_input2.dta " | - sed 's@degenerate_cases/@@g' | - egrep -v 'TOPP_OpenSwathAnalyzer_test_3"|TOPP_OpenSwathAnalyzer_test_4"' | - sed 's/\("TOPP_SiriusAdapter_4".*\)-sirius:database all\(.*\)/\1-sirius:database pubchem\2/' | - grep -v '"TOPP_SiriusAdapter_10"') - - # 1st part is a dirty hack to join lines containing a single function call, e.g. - # addtest(.... - # ....) - echo "$CMAKE" | sed 's/#.*//; s/^\s*//; s/\s*$//' | grep -v "^#" | grep -v "^$" | awk '{printf("%s@NEWLINE@", $0)}' | sed 's/)@NEWLINE@/)\n/g' | sed 's/@NEWLINE@/ /g' | - grep -iE "add_test\(\"(TOPP|UTILS)_.*/$id " | egrep -v "_prepare\"|_convert|WRITEINI|WRITECTD|INVALIDVALUE" | while read -r line - do - line=$(echo "$line" | sed 's/add_test("\([^"]\+\)"/\1/; s/)$//; s/\${TOPP_BIN_PATH}\///g;s/\${DATA_DIR_TOPP}\///g; s#THIRDPARTY/##g') - # >&2 echo $line - test_id=$(echo "$line" | cut -d" " -f 1) - tool_id=$(echo "$line" | cut -d" " -f 2) - # >&2 echo "test_id $test_id" - if [[ $test_id =~ _out_?[0-9]? ]]; then - >&2 echo " skip $test_id $line" - continue - fi - if [[ ${id,,} != ${tool_id,,} ]]; then - >&2 echo " skip $test_id ($id != $tool_id) $line" - continue - fi - - #remove tests with set_tests_properties(....PROPERTIES WILL_FAIL 1) - if grep -lq "$test_id"'\".* PROPERTIES WILL_FAIL 1' $OPENMSGIT/src/tests/topp/CMakeLists.txt $OPENMSGIT/src/tests/topp/THIRDPARTY/third_party_tests.cmake; then - >&2 echo " skip failing "$test_id - continue - fi - tes=" <test>\n" - line=$(fix_tmp_files "$line") - line=$(unique_files "$line") - # >&2 echo LINE $line - #if there is an ini file then we use this to generate the test - #otherwise the ctd file is used - #other command line parameters are inserted later into this xml - if grep -lq "\-ini" <<<"$line"; then - ini=$(echo $line | sed 's/.*-ini \([^ ]\+\).*/\1/') - ini="test-data/$ini" - else - ini="ctd/$tool_id.ctd" - fi - # >&2 echo "========================================================" - # >&2 echo "USING ini $ini" - cli=$(echo $line |cut -d" " -f3- | sed 's/-ini [^ ]\+//') - - ctdtmp=$(mktemp) - # using eval: otherwise for some reason quoted values are not used properly ('A B' -> ["'A", "B'"]) - # >&2 echo "python3 fill_ctd_clargs.py --ini_file $ini $cli" - eval "python3 fill_ctd_clargs.py --ini_file $ini $cli" > "$ctdtmp" - # >&2 echo $ctdtmp - # >&2 cat $ctdtmp - testtmp=$(mktemp) - # >&2 echo CTDConverter galaxy -i $ctdtmp -o $testtmp -s aux/tools_blacklist.txt -f "$FILETYPES" -m macros.xml -t tool.conf -p aux/hardcoded_params.json --tool-version $VERSION --test-only --test-unsniffable csv tsv txt dta dta2d edta mrm splib --test-condition "compare=sim_size" "delta_frac=0.7" - CTDConverter galaxy -i $ctdtmp -o $testtmp -s aux/tools_blacklist.txt -f "$FILETYPES" -m macros.xml -t tool.conf -p aux/hardcoded_params.json --tool-version $VERSION --test-only --test-unsniffable csv tsv txt dta dta2d edta mrm splib --test-condition "compare=sim_size" "delta_frac=0.7" > /dev/null - echo "<!-- $test_id -->" - cat $testtmp | grep -v '<output.*file=""' # | grep -v 'CHEMISTRY/' - - rm "$ctdtmp" "$testtmp" - - #> /dev/null - - #rm $testtmp - done - echo '</xml>' -} - -#some tests use the same file twice which does not work in planemo tests -#hence we create symlinks for each file used twice -function unique_files { - line=$@ - for arg in $@ - do - if [[ ! -f "test-data/$arg" ]]; then - continue - fi - cnt=$(grep -c $arg <<< $(echo "$line" | tr ' ' '\n')) - while [[ $cnt -gt 1 ]]; do - new_arg=$(echo $arg | sed "s/\(.*\)\./\1_$cnt./") - ln -fs $arg test-data/$new_arg - line=$(echo $line | sed "s/\($arg.*\)$arg/\1$new_arg/") - cnt=$(grep -c $arg <<< $(echo "$line" | tr ' ' '\n')) - done - done - - echo $line -} - -# options of out_type selects need to be fixed to Galaxy data types -function fix_out_type { - grep "^$1" "$2" | awk '{print $2}' -} - -#OpenMS tests output to tmp files and compare with FuzzyDiff to the expected file. -#problem: the extension of the tmp files is unusable for test generation. -#unfortunately the extensions used in the DIFF lines are not always usable for the CLI -#(e.g. for prepare_test_data, e.g. CLI expects csv but test file is txt) -#this function replaces the tmp file by the expected file. -function fix_tmp_files { - # >&2 echo "FIX $line" - ret="" - for a in $@; do - # >&2 echo " a "$a - if [[ ! $a =~ .tmp$ ]] && [[ ! $a =~ _tmp_ ]]; then - ret="$ret $a" - continue - fi - diff_line=$(cat $OPENMSGIT/src/tests/topp/CMakeLists.txt $OPENMSGIT/src/tests/topp/THIRDPARTY/third_party_tests.cmake | awk '{printf("%s@NEWLINE@", $0)}' | sed 's/)@NEWLINE@/)\n/g' | sed 's/@NEWLINE@/ /g' | grep '\${DIFF}.*'"$a") - # >&2 echo " diff_line "$diff_line - in1=$(sed 's/.*-in1 \([^ ]\+\).*/\1/' <<<$diff_line) - # >&2 echo " in1 "$in1 - if [[ "$a" != "$in1" ]]; then - ret="$ret $a" - continue - fi - in2=$(sed 's/.*-in2 \([^ ]\+\).*/\1/' <<<$diff_line) - in2=$(basename $in2 | sed 's/)$//') - # >&2 echo " in2 "$in2 - if [[ -f "test-data/$in2" ]]; then - ln -fs "$in1" "test-data/$in2" - ret="$ret $in2" - else - ret="$ret $a" - fi - done -# >&2 echo "--> $ret" - echo "$ret" -} - -function link_tmp_files { - # note this also considers commented lines (starting with a #) - # because of tests where the diff command is commented and we - # still want to use the extension of these files - cat $OPENMSGIT/src/tests/topp/CMakeLists.txt $OPENMSGIT/src/tests/topp/THIRDPARTY/third_party_tests.cmake | sed 's/^\s*//; s/\s*$//' | grep -v "^$" | awk '{printf("%s@NEWLINE@", $0)}' | sed 's/)@NEWLINE@/)\n/g' | sed 's/@NEWLINE@/ /g' | grep "\${DIFF}" | while read -r line - do - in1=$(sed 's/.*-in1 \([^ ]\+\).*/\1/' <<<$line) - in1=$(basename $in1 | sed 's/)$//') - in2=$(sed 's/.*-in2 \([^ ]\+\).*/\1/' <<<$line) - in2=$(basename $in2 | sed 's/)$//') - if [[ "$in1" == "$in2" ]]; then - >&2 echo "not linking equal $in1 $in2" - continue - fi - ln -f -s $in1 test-data/$in2 - done - - find test-data/ -name "*.tmp" -print0 | - while IFS= read -r -d '' i; do - if [ ! -e test-data/$(basename $i .tmp) ]; then - ln -s $(basename $i) test-data/$(basename $i .tmp) - else - ln -fs $(basename $i) test-data/$(basename $i .tmp) - fi - done -} - - - -# parse data preparation calls from OpenMS sources for a tool with a given id -function prepare_test_data { -# id=$1 -# | egrep -i "$id\_.*[0-9]+(_prepare\"|_convert)?" - - # TODO SiriusAdapter depends on online service which may timeout .. so keep disabled https://github.com/OpenMS/OpenMS/pull/5010 - cat $OPENMSGIT/src/tests/topp/CMakeLists.txt $OPENMSGIT/src/tests/topp/THIRDPARTY/third_party_tests.cmake | sed 's/#.*$//'| sed 's/^\s*//; s/\s*$//' | grep -v "^$" | awk '{printf("%s@NEWLINE@", $0)}' | sed 's/)@NEWLINE@/)\n/g' | sed 's/@NEWLINE@/ /g' | - sed 's/degenerate_cases\///' | - egrep -v "WRITEINI|WRITECTD|INVALIDVALUE|DIFF" | - grep add_test | - egrep "TOPP|UTILS" | - sed 's@${DATA_DIR_SHARE}/@@g;'| - sed 's@${TMP_RIP_PATH}@./@g'| - sed 's@TOFCalibration_ref_masses @TOFCalibration_ref_masses.txt @g; s@TOFCalibration_const @TOFCalibration_const.csv @'| - sed 's/\("TOPP_SiriusAdapter_4".*\)-sirius:database all\(.*\)/\1-sirius:database pubchem\2/' | - while read line - do - test_id=$(echo "$line" | sed 's/add_test(//; s/"//g; s/)[^)]*$//; s/\${TOPP_BIN_PATH}\///g;s/\${DATA_DIR_TOPP}\///g; s#THIRDPARTY/##g' | cut -d" " -f1) - - if grep -lq "$test_id"'\".* PROPERTIES WILL_FAIL 1' $OPENMSGIT/src/tests/topp/CMakeLists.txt $OPENMSGIT/src/tests/topp/THIRDPARTY/third_party_tests.cmake; then - >&2 echo " skip failing "$test_id - continue - fi - - line=$(echo "$line" | sed 's/add_test("//; s/)[^)]*$//; s/\${TOPP_BIN_PATH}\///g;s/\${DATA_DIR_TOPP}\///g; s#THIRDPARTY/##g' | cut -d" " -f2-) - # line="$(fix_tmp_files $line)" - echo 'echo executing "'$test_id'"' - echo "$line > $test_id.stdout 2> $test_id.stderr" - echo "if [[ \"\$?\" -ne \"0\" ]]; then >&2 echo '$test_id failed'; >&2 echo -e \"stderr:\n\$(cat $test_id.stderr | sed 's/^/ /')\"; echo -e \"stdout:\n\$(cat $test_id.stdout)\";fi" - done -}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/get_tests.py Fri Jun 14 21:31:16 2024 +0000 @@ -0,0 +1,344 @@ +#!/usr/bin/env python + +import argparse +import os.path +import re +import shlex +import sys +import tempfile +from typing import ( + Dict, + List, + Optional, + TextIO, + Tuple, +) + +from ctdconverter.common.utils import ( + ParameterHardcoder, + parse_hardcoded_parameters, + parse_input_ctds, +) +from ctdconverter.galaxy.converter import convert_models +from CTDopts.CTDopts import ( + CTDModel, + ModelTypeError, + Parameters, +) + +SKIP_LIST = [ + r"_prepare\"", + r"_convert", + r"WRITEINI", + r"WRITECTD", + r"INVALIDVALUE", + r"\.ini\.json", + r"OpenSwathMzMLFileCacher .*-convert_back", # - OpenSwathMzMLFileCacher with -convert_back argument https://github.com/OpenMS/OpenMS/issues/4399 + r"MaRaClusterAdapter.*-consensus_out", # - MaRaCluster with -consensus_out (parameter blacklister: https://github.com/OpenMS/OpenMS/issues/4456) + r"FileMerger_1_input1.dta2d.*FileMerger_1_input2.dta ", # - FileMerger with mixed dta dta2d input (ftype can not be specified in the test, dta can not be sniffed) + r'^(TOPP_OpenSwathAnalyzer_test_3|TOPP_OpenSwathAnalyzer_test_4)$', # no suppert for cached mzML + r'TOPP_SiriusAdapter_[0-9]+$', # Do not test SiriusAdapter https://github.com/OpenMS/OpenMS/issues/7000 .. will be removed anyway + r'TOPP_AssayGeneratorMetabo_(7|8|9|10|11|12|13|14|15|16|17|18)$' # Skip AssayGeneratorMetabo tests using Sirius https://github.com/OpenMS/OpenMS/issues/7150 (will be replaced by two tools) +] + + +def get_failing_tests(cmake: List[str]) -> List[str]: + failing_tests = [] + re_fail = re.compile(r"set_tests_properties\(\"([^\"]+)\" PROPERTIES WILL_FAIL 1\)") + + for cmake in args.cmake: + with open(cmake) as cmake_fh: + for line in cmake_fh: + match = re_fail.search(line) + if match: + failing_tests.append(match.group(1)) + return failing_tests + + +def fix_tmp_files(line: str, diff_pairs: Dict[str, str]) -> str: + """ + OpenMS tests output to tmp files and compare with FuzzyDiff to the expected file. + problem: the extension of the tmp files is unusable for test generation. + unfortunately the extensions used in the DIFF lines are not always usable for the CLI + (e.g. for prepare_test_data, e.g. CLI expects csv but test file is txt) + this function replaces the tmp file by the expected file. + """ + cmd = shlex.split(line) + for i, e in enumerate(cmd): + if e in diff_pairs: + dst = os.path.join("test-data", diff_pairs[e]) + if os.path.exists(dst): + os.unlink(dst) + sys.stderr.write(f"symlink {e} {dst}\n") + os.symlink(e, dst) + cmd[i] = diff_pairs[e] + return shlex.join(cmd) + + +def get_ini(line: str, tool_id: str) -> Tuple[str, str]: + """ + if there is an ini file then we use this to generate the test + otherwise the ctd file is used + other command line parameters are inserted later into this xml + """ + cmd = shlex.split(line) + ini = None + for i, e in enumerate(cmd): + if e == "-ini": + ini = cmd[i + 1] + cmd = cmd[:i] + cmd[i + 2:] + if ini: + return os.path.join("test-data", ini), shlex.join(cmd) + else: + return os.path.join("ctd", f"{tool_id}.ctd"), line + + +def unique_files(line: str): + """ + some tests use the same file twice which does not work in planemo tests + hence we create symlinks for each file used twice + """ + cmd = shlex.split(line) + # print(f"{cmd}") + files = {} + # determine the list of indexes where each file argument (anything appearing in test-data/) appears + for idx, e in enumerate(cmd): + p = os.path.join("test-data", e) + if not os.path.exists(p) and not os.path.islink(p): + continue + try: + files[e].append(idx) + except KeyError: + files[e] = [idx] + # print(f"{files=}") + for f in files: + if len(files[f]) < 2: + continue + for i, idx in enumerate(files[f]): + f_parts = f.split(".") + f_parts[0] = f"{f_parts[0]}_{i}" + new_f = ".".join(f_parts) + # if os.path.exists(os.path.join("test-data", new_f)): + # os.unlink(os.path.join("test-data", new_f)) + sys.stderr.write( + f'\tsymlink {os.path.join("test-data", new_f)} {f}\n' + ) + try: + os.symlink(f, os.path.join("test-data", new_f)) + except FileExistsError: + pass + cmd[idx] = new_f + return shlex.join(cmd) + + +def fill_ctd_clargs(ini: str, line: str, ctd_tmp: TextIO) -> None: + cmd = shlex.split(line) + + # load CTDModel + ini_model = None + try: + ini_model = CTDModel(from_file=ini) + except ModelTypeError: + pass + try: + ini_model = Parameters(from_file=ini) + except ModelTypeError: + pass + assert ini_model is not None, "Could not parse %s, seems to be no CTD/PARAMS" % ( + args.ini_file + ) + + # get a dictionary of the ctd arguments where the values of the parameters + # given on the command line are overwritten + ini_values = ini_model.parse_cl_args(cl_args=cmd, ignore_required=True) + ini_model.write_ctd(ctd_tmp, ini_values) + + +def process_test_line( + id: str, + line: str, + failing_tests: List[str], + skip_list: List[str], + diff_pairs: Dict[str, str], +) -> Optional[str]: + + re_test_id = re.compile(r"add_test\(\"([^\"]+)\" ([^ ]+) (.*)") + re_id_out_test = re.compile(r"_out_?[0-9]?") + + # TODO auto extract from set(OLD_OSW_PARAM ... lin + line = line.replace( + "${OLD_OSW_PARAM}", + " -test -mz_extraction_window 0.05 -mz_extraction_window_unit Th -ms1_isotopes 0 -Scoring:TransitionGroupPicker:compute_peak_quality -Scoring:Scores:use_ms1_mi false -Scoring:Scores:use_mi_score false", + ) + + line = line.replace("${TOPP_BIN_PATH}/", "") + line = line.replace("${DATA_DIR_TOPP}/", "") + line = line.replace("THIRDPARTY/", "") + line = line.replace("${DATA_DIR_SHARE}/", "") + # IDRipper PATH gets empty causing problems. TODO But overall the option needs to be handled differently + line = line.replace("${TMP_RIP_PATH}/", "") + # some input files are originally in a subdir (degenerated cases/), but not in test-data + line = line.replace("degenerate_cases/", "") + # determine the test and tool ids and remove the 1) add_test("TESTID" 2) trailing ) + match = re_test_id.match(line) + if not match: + sys.exit(f"Ill formated test line {line}\n") + test_id = match.group(1) + tool_id = match.group(2) + + line = f"{match.group(2)} {match.group(3)}" + + if test_id in failing_tests: + sys.stderr.write(f" skip failing {test_id} {line}\n") + return + + if id != tool_id: + sys.stderr.write(f" skip {test_id} ({id} != {tool_id}) {line}\n") + return + + if re_id_out_test.search(test_id): + sys.stderr.write(f" skip {test_id} {line}\n") + return + + for skip in skip_list: + if re.search(skip, line): + return + if re.search(skip, test_id): + return + + line = fix_tmp_files(line, diff_pairs) + # print(f"fix {line=}") + line = unique_files(line) + # print(f"unq {line=}") + ini, line = get_ini(line, tool_id) + + from dataclasses import dataclass, field + + @dataclass + class CTDConverterArgs: + input_files: list + output_destination: str + default_executable_path: Optional[str] = None + hardcoded_parameters: Optional[str] = None + parameter_hardcoder: Optional[ParameterHardcoder] = None + xsd_location: Optional[str] = None + formats_file: Optional[str] = None + add_to_command_line: str = "" + required_tools_file: Optional[str] = None + skip_tools_file: Optional[str] = None + macros_files: Optional[List[str]] = field(default_factory=list) + test_macros_files: Optional[List[str]] = field(default_factory=list) + test_macros_prefix: Optional[List[str]] = field(default_factory=list) + test_test: bool = False + test_only: bool = False + test_unsniffable: Optional[List[str]] = field(default_factory=list) + test_condition: Optional[List[str]] = ("compare=sim_size", "delta_frac=0.05") + tool_version: str = None + tool_profile: str = None + bump_file: str = None + + # create an ini/ctd file where the values are equal to the arguments from the command line + # and transform it to xml + test = [f"<!-- {test_id} -->\n"] + with tempfile.NamedTemporaryFile( + mode="w+", delete_on_close=False + ) as ctd_tmp, tempfile.NamedTemporaryFile( + mode="w+", delete_on_close=False + ) as xml_tmp: + fill_ctd_clargs(ini, line, ctd_tmp) + ctd_tmp.close() + xml_tmp.close() + parsed_ctd = parse_input_ctds(None, [ctd_tmp.name], xml_tmp.name, "xml") + ctd_args = CTDConverterArgs( + input_files=[ctd_tmp.name], + output_destination=xml_tmp.name, + macros_files=["macros.xml"], + skip_tools_file="aux/tools_blacklist.txt", + formats_file="aux/filetypes.txt", + # tool_conf_destination = "tool.conf", + hardcoded_parameters="aux/hardcoded_params.json", + tool_version="3.1", + test_only=True, + test_unsniffable=[ + "csv", + "tsv", + "txt", + "dta", + "dta2d", + "edta", + "mrm", + "splib", + ], + test_condition=["compare=sim_size", "delta_frac=0.7"], + ) + ctd_args.parameter_hardcoder = parse_hardcoded_parameters( + ctd_args.hardcoded_parameters + ) + convert_models(ctd_args, parsed_ctd) + xml_tmp = open(xml_tmp.name, "r") + for l in xml_tmp: + test.append(l) + + return "".join(test) + + +parser = argparse.ArgumentParser(description="Create Galaxy tests for a OpenMS tools") +parser.add_argument("--id", dest="id", help="tool id") +parser.add_argument("--cmake", nargs="+", help="OpenMS test CMake files") +args = parser.parse_args() +sys.stderr.write(f"generate tests for {args.id}\n") + +re_comment = re.compile("#.*") +re_empty_prefix = re.compile(r"^\s*") +re_empty_suffix = re.compile(r"\s*$") +re_add_test = re.compile(r"add_test\(\"(TOPP|UTILS)_.*/" + args.id) +re_diff = re.compile(r"\$\{DIFF\}.* -in1 ([^ ]+) -in2 ([^ ]+)") +failing_tests = get_failing_tests(args.cmake) +tests = [] + +# process the given CMake files and compile lists of +# - test lines .. essentially add_test(...) +# - and pairs of files that are diffed +jline = "" +test_lines = [] +diff_pairs = {} +for cmake in args.cmake: + with open(cmake) as cmake_fh: + for line in cmake_fh: + # remove comments, empty prefixes and suffixes + line = re_comment.sub("", line) + line = re_empty_prefix.sub("", line) + line = re_empty_suffix.sub("", line) + # skip empty lines + if line == "": + continue + + # join test statements that are split over multiple lines + if line.endswith(")"): + jline += " " + line[:-1] + else: + jline = line + continue + line, jline = jline.strip(), "" + match = re_diff.search(line) + if match: + in1 = match.group(1).split("/")[-1] + in2 = match.group(2).split("/")[-1] + if in1 != in2: + diff_pairs[in1] = in2 + elif re_add_test.match(line): + test_lines.append(line) + +for line in test_lines: + test = process_test_line(args.id, line, failing_tests, SKIP_LIST, diff_pairs) + if test: + tests.append(test) + +tests = "\n".join(tests) +print( + f""" +<xml name="autotest_{args.id}"> +{tests} +</xml> +""" +)
--- a/macros.xml Thu Dec 01 19:13:13 2022 +0000 +++ b/macros.xml Fri Jun 14 21:31:16 2024 +0000 @@ -3,19 +3,19 @@ You can edit this file to add your own macros, if you so desire, or you can add additional macro files using the m/macros parameter --> <macros> - <token name="@TOOL_VERSION@">2.8</token> + <token name="@TOOL_VERSION@">3.1</token> <token name="@VERSION_SUFFIX@">0</token> + <token name="@TEST_DATA_LOCATION@"/> <xml name="requirements"> <requirements> <requirement type="package" version="@TOOL_VERSION@">openms</requirement> <requirement type="package" version="@TOOL_VERSION@">openms-thirdparty</requirement> <!-- omssa (which has been excluded from 3rdparty) and makeblastdb for OMSSAAdapter --> - <requirement type="package" version="2.1.9">omssa</requirement> - <requirement type="package" version="2.13.0">blast</requirement> + <requirement type="package" version="2.14.1">blast</requirement> <!--<requirement type="package" version="5.0.0">tpp</requirement>--> <!-- for realpath (used e.g. in LuciphorAdapter) --> <!--<requirement type="package" version="8.25">coreutils</requirement>--> - <requirement type="package" version="1.4">ctdopts</requirement> + <requirement type="package" version="1.5">ctdopts</requirement> <yield/> </requirements> </xml> @@ -26,6 +26,8 @@ <regex match="Could not allocate metaspace" level="fatal_oom" description="Java memory Exception"/> <regex match="Cannot create VM thread" level="fatal_oom" description="Java memory Exception"/> <regex match="qUncompress: could not allocate enough memory to uncompress data" level="fatal_oom" description="Java memory Exception"/> + <regex match="OMSSA ran out of RAM" level="fatal_oom" description="Could not allocate memory"/> + <regex match="comet' crashed hard (segfault-like). Please check the log." level="fatal_oom" description="Could not allocate memory"/> </stdio> </xml> <xml name="references"> @@ -113,11 +115,11 @@ </token> <token name="@EXT_FOO@"><![CDATA[#def oms2gxyext(o) - #set m={'txt': 'txt', 'tsv': 'tabular', 'bioml': 'xml', 'consensusXML': 'consensusxml', 'csv': 'csv', 'dta': 'dta', 'dta2d': 'dta2d', 'edta': 'edta', 'fa': 'fasta', 'fas': 'fasta', 'fasta': 'fasta', 'FASTA': 'fasta', 'featureXML': 'featurexml', 'featurexml': 'featurexml', 'html': 'html', 'HTML': 'html', 'idXML': 'idxml', 'json': 'json', 'kroenik': 'kroenik', 'mascotXML': 'mascotxml', 'mgf': 'mgf', 'mrm': 'mrm', 'ms': 'sirius.ms', 'ms2': 'ms2', 'msp': 'msp', 'mzData': 'mzdata', 'mzid': 'mzid', 'mzML': 'mzml', 'mzml': 'mzml', 'mzq': 'mzq', 'mzQC': 'mzqc', 'mzTab': 'mztab', 'mzXML': 'mzxml', 'novor': 'txt', 'obo': 'obo', 'oms': 'sqlite', 'omssaXML': 'idxml', 'osw': 'osw', 'OSW': 'osw', 'params': 'txt', 'paramXML': 'paramxml', 'peplist': 'peplist', 'pep.xml': 'pepxml', 'pepXML': 'pepxml', 'png': 'png', 'PNG': 'png', 'protXML': 'protxml', 'psms': 'psms', 'pqp': 'pqp', 'qcML': 'qcml', 'spec.xml': 'spec.xml', 'splib': 'splib', 'sqMass': 'sqmass', 'tandem.xml': 'tandem', 'trafoXML': 'trafoxml', 'traML': 'traml', 'TraML': 'traml', 'tab': 'tabular', 'raw': 'thermo.raw', 'xls': 'tsv', 'XML': 'xml', 'xml': 'xml', 'xquest.xml': 'xquest.xml', 'xsd': 'xml'} + #set m={'txt': 'txt', 'tsv': 'tabular', 'bioml': 'xml', 'consensusXML': 'consensusxml', 'csv': 'csv', 'dta': 'dta', 'dta2d': 'dta2d', 'edta': 'edta', 'fa': 'fasta', 'fas': 'fasta', 'fasta': 'fasta', 'FASTA': 'fasta', 'featureXML': 'featurexml', 'featurexml': 'featurexml', 'html': 'html', 'HTML': 'html', 'idXML': 'idxml', 'json': 'json', 'kroenik': 'kroenik', 'mascotXML': 'mascotxml', 'mgf': 'mgf', 'mrm': 'mrm', 'ms': 'sirius.ms', 'ms2': 'ms2', 'msp': 'msp', 'mzData': 'mzdata', 'mzid': 'mzid', 'mzML': 'mzml', 'mzml': 'mzml', 'mzq': 'mzq', 'mzQC': 'mzqc', 'mzTab': 'mztab', 'mzXML': 'mzxml', 'novor': 'txt', 'obo': 'obo', 'oms': 'sqlite', 'omssaXML': 'idxml', 'osw': 'osw', 'OSW': 'osw', 'params': 'txt', 'paramXML': 'paramxml', 'peplist': 'peplist', 'pep.xml': 'pepxml', 'pepXML': 'pepxml', 'png': 'png', 'PNG': 'png', 'protXML': 'protxml', 'psms': 'psms', 'pqp': 'pqp', 'qcML': 'qcml', 'spec.xml': 'spec.xml', 'splib': 'splib', 'sqMass': 'sqmass', 'tandem.xml': 'tandem', 'trafoXML': 'trafoxml', 'traML': 'traml', 'TraML': 'traml', 'tab': 'tabular', 'raw': 'thermo.raw', 'xls': 'tsv', 'XML': 'xml', 'xml': 'xml', 'xquest.xml': 'xquest.xml', 'xsd': 'xsd', 'zip': 'zip'} #return m[o] #end def #def gxy2omsext(g) - #set m={'txt': 'txt', 'tabular': 'tsv', 'xml': 'bioml', 'consensusxml': 'consensusXML', 'csv': 'csv', 'dta': 'dta', 'dta2d': 'dta2d', 'edta': 'edta', 'fasta': 'fa', 'featurexml': 'featureXML', 'html': 'html', 'idxml': 'idXML', 'json': 'json', 'kroenik': 'kroenik', 'mascotxml': 'mascotXML', 'mgf': 'mgf', 'mrm': 'mrm', 'sirius.ms': 'ms', 'ms2': 'ms2', 'msp': 'msp', 'mzdata': 'mzData', 'mzid': 'mzid', 'mzml': 'mzML', 'mzq': 'mzq', 'mzqc': 'mzQC', 'mztab': 'mzTab', 'mzxml': 'mzXML', 'obo': 'obo', 'sqlite': 'oms', 'osw': 'osw', 'paramxml': 'paramXML', 'peff': 'fasta', 'peplist': 'peplist', 'pepxml': 'pep.xml', 'png': 'png', 'protxml': 'protXML', 'psms': 'psms', 'pqp': 'pqp', 'qcml': 'qcML', 'spec.xml': 'spec.xml', 'splib': 'splib', 'sqmass': 'sqMass', 'tandem': 'tandem.xml', 'trafoxml': 'trafoXML', 'traml': 'traML', 'thermo.raw': 'raw', 'tsv': 'xls', 'xquest.xml': 'xquest.xml'} + #set m={'txt': 'txt', 'tabular': 'tsv', 'xml': 'bioml', 'consensusxml': 'consensusXML', 'csv': 'csv', 'dta': 'dta', 'dta2d': 'dta2d', 'edta': 'edta', 'fasta': 'fa', 'featurexml': 'featureXML', 'html': 'html', 'idxml': 'idXML', 'json': 'json', 'kroenik': 'kroenik', 'mascotxml': 'mascotXML', 'mgf': 'mgf', 'mrm': 'mrm', 'sirius.ms': 'ms', 'ms2': 'ms2', 'msp': 'msp', 'mzdata': 'mzData', 'mzid': 'mzid', 'mzml': 'mzML', 'mzq': 'mzq', 'mzqc': 'mzQC', 'mztab': 'mzTab', 'mzxml': 'mzXML', 'obo': 'obo', 'sqlite': 'oms', 'osw': 'osw', 'paramxml': 'paramXML', 'peff': 'fasta', 'peplist': 'peplist', 'pepxml': 'pep.xml', 'png': 'png', 'protxml': 'protXML', 'psms': 'psms', 'pqp': 'pqp', 'qcml': 'qcML', 'spec.xml': 'spec.xml', 'splib': 'splib', 'sqmass': 'sqMass', 'tandem': 'tandem.xml', 'trafoxml': 'trafoXML', 'traml': 'traML', 'thermo.raw': 'raw', 'tsv': 'xls', 'xquest.xml': 'xquest.xml', 'xsd': 'xsd', 'zip': 'zip'} #return m[g] #end def ]]></token></macros>
--- a/prepare_test_data_manual.sh Thu Dec 01 19:13:13 2022 +0000 +++ b/prepare_test_data_manual.sh Fri Jun 14 21:31:16 2024 +0000 @@ -1,8 +1,3 @@ -MSSimulator -test -in DecoyDatabase_1.fasta -out MSsimulator.mzml -algorithm:RandomNumberGenerators:biological reproducible -algorithm:RandomNumberGenerators:technical reproducible > MSSimulator_1.stdout 2> stderr -if [[ "$?" -ne "0" ]]; then >&2 echo 'MSSimulator_1 failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi - -MSSimulator -test -in DecoyDatabase_1.fasta -out MSsimulator_MALDI.mzml -algorithm:RandomNumberGenerators:biological reproducible -algorithm:RandomNumberGenerators:technical reproducible -algorithm:MSSim:Global:ionization_type MALDI > MSSimulator_2.stdout 2> stderr -if [[ "$?" -ne "0" ]]; then >&2 echo 'MSSimulator_2 failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi ClusterMassTracesByPrecursor -test -in_ms1 ConsensusMapNormalizer_input.consensusXML -in_swath ConsensusMapNormalizer_input.consensusXML -out ClusterMassTracesByPrecursor.mzml > ClusterMassTracesByPrecursor.stdout 2> stderr if [[ "$?" -ne "0" ]]; then >&2 echo 'ClusterMassTracesByPrecursor failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi @@ -13,8 +8,7 @@ CVInspector -test -cv_files CHEMISTRY/XLMOD.obo -cv_names XLMOD -mapping_file MAPPING/ms-mapping.xml -html CVInspector.html > CVInspector.stdout 2> stderr if [[ "$?" -ne "0" ]]; then >&2 echo 'CVInspector failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi -DeMeanderize -test -in MSsimulator_MALDI.mzml -out DeMeanderize.mzml > DeMeanderize.stdout 2> stderr -if [[ "$?" -ne "0" ]]; then >&2 echo 'DeMeanderize failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi +# TODO DeMeanderize # TODO DigestorMotif @@ -30,26 +24,17 @@ if [[ "$?" -ne "0" ]]; then >&2 echo 'FeatureFinderIsotopeWavelet failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi -FFEval -test -in FeatureFinderCentroided_1_output.featureXML -truth FeatureFinderCentroided_1_output.featureXML -out FFEval.featureXML -out_roc FFEval_roc.csv > FFEval.stdout 2> stderr -if [[ "$?" -ne "0" ]]; then >&2 echo 'FFEval failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi - # TODO? deprecated IDDecoyProbability IDExtractor -test -in MSGFPlusAdapter_1_out.idXML -best_hits -number_of_peptides 1 -out IDExtractor.idXML > IDExtractor.stdout 2> stderr if [[ "$?" -ne "0" ]]; then >&2 echo 'IDExtractor failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi -LabeledEval -test -in FeatureLinkerLabeled_1_input.featureXML -truth FeatureLinkerLabeled_1_output.consensusXML> LabeledEval.txt > LabeledEval.stdout 2> stderr -if [[ "$?" -ne "0" ]]; then >&2 echo 'LabeledEval failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi - MapStatistics -test -in SiriusAdapter_3_input.featureXML -out MapStatistics.txt > MapStatistics_1.stdout 2> stderr if [[ "$?" -ne "0" ]]; then >&2 echo 'MapStatistics_1 failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi MapStatistics -test -in ConsensusXMLFile_1.consensusXML -out MapStatistics2.txt > MapStatistics_2.stdout 2> stderr if [[ "$?" -ne "0" ]]; then >&2 echo 'MapStatistics_2 failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi -MetaboliteAdductDecharger -test -in Decharger_input.featureXML -out_cm MetaboliteAdductDecharger_cm.consensusXML -out_fm MetaboliteAdductDecharger_fm.featureXML -outpairs MetaboliteAdductDecharger_pairs.consensusXML > MetaboliteAdductDecharger.stdout 2> stderr -if [[ "$?" -ne "0" ]]; then >&2 echo 'MetaboliteAdductDecharger failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi - MetaboliteSpectralMatcher -test -in spectra.mzML -database MetaboliteSpectralDB.mzML -out MetaboliteSpectralMatcher.mzTab > MetaboliteSpectralMatcher.stdout 2> stderr if [[ "$?" -ne "0" ]]; then >&2 echo 'MetaboliteSpectralMatcher failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi @@ -68,20 +53,6 @@ OpenSwathRewriteToFeatureXML -featureXML OpenSwathFeatureXMLToTSV_input.featureXML -out OpenSwathRewriteToFeatureXML.featureXML > OpenSwathRewriteToFeatureXML.stdout 2> stderr # if [[ "$?" -ne "0" ]]; then >&2 echo 'OpenSwathRewriteToFeatureXML failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi -# adapted from the commented tests in OpenMS TODO may be removed later https://github.com/OpenMS/OpenMS/issues/4719 -FileConverter -in PepNovo.mzXML -out PepNovo_1.mzML > /dev/null 2> stderr -if [[ "$?" -ne "0" ]]; then >&2 echo 'FileConverter failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi - -PepNovoAdapter -ini PepNovoAdapter_1_parameters.ini -in PepNovo_1.mzML -out PepNovoAdapter_3_output.idXML -model_directory pepnovo_models/ -pepnovo_executable pepnovo > PepNovo_1.stdout 2> stderr -if [[ "$?" -ne "0" ]]; then >&2 echo 'PhosphoScoring failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi - -FileConverter -in PepNovo.mzData -out PepNovo_4.mzML > /dev/null 2> stderr -if [[ "$?" -ne "0" ]]; then >&2 echo 'FileConverter failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi -PepNovoAdapter -ini PepNovoAdapter_1_parameters.ini -in PepNovo_4.mzML -out PepNovoAdapter_4_output.idXML -model_directory pepnovo_models/ -pepnovo_executable pepnovo > PepNovo_1.stdout 2> stderr -if [[ "$?" -ne "0" ]]; then >&2 echo 'PhosphoScoring failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi - -#PepNovoAdapter -ini PepNovoAdapter_5_parameters.ini -in PepNovoAdapter_5_output.pepnovo_out -out PepNovoAdapter_5_output.idXML -model_directory pepnovo_models/ - # TODO PhosphoScoring PhosphoScoring -in spectra.mzML -id MSGFPlusAdapter_1_out1.tmp -out PhosphoScoring.idxml > PhosphoScoring.stdout 2> stderr if [[ "$?" -ne "0" ]]; then >&2 echo 'PhosphoScoring failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi @@ -118,9 +89,6 @@ RNPxlXICFilter -test -control FileFilter_1_input.mzML -treatment FileFilter_1_input.mzML -out RNPxlXICFilter.mzML > RNPxlXICFilter.stdout 2> stderr if [[ "$?" -ne "0" ]]; then >&2 echo 'RNPxlXICFilter failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi -RTEvaluation -in PeptideIndexer_1.idXML -out RTEvaluation.tsv > RTEvaluation.stdout 2> stderr -if [[ "$?" -ne "0" ]]; then >&2 echo 'RTEvaluation failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi - SemanticValidator -test -in FileFilter_1_input.mzML -mapping_file MAPPING/ms-mapping.xml > SemanticValidator.stdout 2> stderr if [[ "$?" -ne "0" ]]; then >&2 echo 'SemanticValidator failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi @@ -152,13 +120,8 @@ SpectraFilterThresholdMower -test -in SpectraFilterSqrtMower_1_input.mzML -out SpectraFilterThresholdMower.mzML > SpectraFilterThresholdMower.stdout 2> stderr if [[ "$?" -ne "0" ]]; then >&2 echo 'SpectraFilterThresholdMower failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi -SpectraMerger -test -in NovorAdapter_in.mzML -out SpectraMerger_1.mzML > SpectraMerger.stdout 2> stderr +SpectraMerger -test -in NovorAdapter_in.mzML -out SpectraMerger_1.mzML -algorithm:average_gaussian:ms_level 2 > SpectraMerger.stdout 2> stderr if [[ "$?" -ne "0" ]]; then >&2 echo 'SpectraMerger failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi -# TODO SvmTheoreticalSpectrumGeneratorTrainer - -TransformationEvaluation -test -in FileInfo_16_input.trafoXML -out TransformationEvaluation.trafoXML > TransformationEvaluation.stdout 2> stderr -if [[ "$?" -ne "0" ]]; then >&2 echo 'TransformationEvaluation failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi - XMLValidator -test -in FileFilter_1_input.mzML > XMLValidator.stdout 2> stderr if [[ "$?" -ne "0" ]]; then >&2 echo 'XMLValidator failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi
--- a/readme.md Thu Dec 01 19:13:13 2022 +0000 +++ b/readme.md Fri Jun 14 21:31:16 2024 +0000 @@ -11,7 +11,7 @@ * https://www.openms.de/ The wrappers for these tools and most of their tests are automatically -generated using the `generate.sh` script. The generation of the tools is +generated using the `./aux/generate.sh` script. The generation of the tools is based on the CTDConverter (https://github.com/WorkflowConversion/CTDConverter) which can be fine tuned via the `hardcoded_params.json` file. This file allows to blacklist and hardcode parameters and to modify or set arbitrary @@ -129,15 +129,6 @@ Open problems ============= -Some tools stall in CI testing using `--biocontainers` which is why the OpenMS -tools are currently listed in `.tt_biocontainer_skip`. This is - -- AssayGeneratorMetabo and SiriusAdapter (both depend on sirius) -- OMSSAAdapter - -Using `docker -t` seems to solve the problem (see -https://github.com/galaxyproject/galaxy/issues/10153). - Licence (MIT) =============
--- a/test-data.sh Thu Dec 01 19:13:13 2022 +0000 +++ b/test-data.sh Fri Jun 14 21:31:16 2024 +0000 @@ -1,11 +1,10 @@ #!/usr/bin/env bash -VERSION=2.8 +# set -x + +VERSION=3.1 FILETYPES="aux/filetypes.txt" -CONDAPKG="https://anaconda.org/bioconda/openms/2.8.0/download/linux-64/openms-2.8.0-h7ca0330_0.tar.bz2" - -# import the magic -. ./generate-foo.sh +CONDAPKG="https://anaconda.org/bioconda/openms/3.1.0/download/linux-64/openms-3.1.0-h8964181_1.tar.bz2" # install conda if [ -z "$tmp" ]; then @@ -45,17 +44,20 @@ echo "Clone OpenMS $VERSION sources" if [[ ! -d $OPENMSGIT ]]; then - # TODO >2.8 reenable original release branch .. also in else branch - # the plus branch contains commits from https://github.com/OpenMS/OpenMS/pull/5920 and https://github.com/OpenMS/OpenMS/pull/5917 - # git clone -b release/$VERSION.0 https://github.com/OpenMS/OpenMS.git $OPENMSGIT - git clone -b release/$VERSION.0-plus https://github.com/bernt-matthias/OpenMS.git $OPENMSGIT - cd $OPENMSGIT - git submodule init - git submodule update - cd - + if [[ "$created" == "yes" ]]; then + GIT_DIR=$(mktemp -d --dry-run) + GIT_EXTRA_OPTS="--separate-git-dir=$GIT_DIR" + fi + git clone -b release/$VERSION.0 --depth 1 --recurse-submodules=THIRDPARTY --shallow-submodules $GIT_EXTRA_OPTS https://github.com/OpenMS/OpenMS.git $OPENMSGIT + ## save some space by just keeping the needed binaries + find $OPENMSGIT/THIRDPARTY/ -type f -not \( -name maracluster -o -name spectrast \) -delete + find $OPENMSGIT/THIRDPARTY/ -empty -type d -delete + if [[ "$created" == "yes" ]]; then + rm -rf $GIT_DIR + fi else cd $OPENMSGIT - git pull origin release/$VERSION.0-plus + git pull origin release/$VERSION.0 cd - fi @@ -65,7 +67,7 @@ if conda env list | grep "$OPENMSENV"; then true else - conda create -y --quiet --override-channels --channel iuc --channel conda-forge --channel bioconda --channel defaults -n $OPENMSENV openms=$VERSION openms-thirdparty=$VERSION omssa=2.1.9 ctdopts=1.5 lxml + conda create -y --quiet --solver libmamba --override-channels --strict-channel-priority --channel conda-forge --channel bioconda -n $OPENMSENV openms=$VERSION openms-thirdparty=$VERSION ctdopts=1.5 lxml # chmod -R u-w $OPENMSENV fi ############################################################################### @@ -101,33 +103,34 @@ conda deactivate -# ############################################################################### -# ## copy all the test data files to test-data -# ## most of it (outputs) will be overwritten later, but its needed for -# ## prepare_test_data -# ############################################################################### +# # ############################################################################### +# # ## copy all the test data files to test-data +# # ## most of it (outputs) will be overwritten later, but its needed for +# # ## prepare_test_data +# # ############################################################################### echo "Get test data" -find test-data -type f,l,d ! -name "*fa" ! -name "*loc" ! -name "test-data" -delete +find test-data -type f,l,d ! -name "*fa" ! -name "*loc" ! -name "test-data" ! -name MetaboliteSpectralDB.mzML -delete cp $(find $OPENMSGIT/src/tests/topp/ -type f | grep -Ev "third_party_tests.cmake|CMakeLists.txt|check_ini") test-data/ cp -r $OPENMSGIT/share/OpenMS/MAPPING/ test-data/ cp -r $OPENMSGIT/share/OpenMS/CHEMISTRY test-data/ cp -r $OPENMSGIT/share/OpenMS/examples/ test-data/ if [ ! -f test-data/MetaboliteSpectralDB.mzML ]; then - wget -nc https://abibuilder.cs.uni-tuebingen.de/archive/openms/Tutorials/Data/latest/Example_Data/Metabolomics/databases/MetaboliteSpectralDB.mzML + wget -nc https://raw.githubusercontent.com/sneumann/OpenMS/master/share/OpenMS/CHEMISTRY/MetaboliteSpectralDB.mzML + # wget -nc https://abibuilder.cs.uni-tuebingen.de/archive/openms/Tutorials/Data/latest/Example_Data/Metabolomics/databases/MetaboliteSpectralDB.mzML mv MetaboliteSpectralDB.mzML test-data/ fi ln -fs TOFCalibration_ref_masses test-data/TOFCalibration_ref_masses.txt ln -fs TOFCalibration_const test-data/TOFCalibration_const.csv -if [ ! -d test-data/pepnovo_models/ ]; then - mkdir -p /tmp/pepnovo - wget -nc http://proteomics.ucsd.edu/Software/PepNovo/PepNovo.20120423.zip - unzip PepNovo.20120423.zip -d /tmp/pepnovo/ - mv /tmp/pepnovo/Models test-data/pepnovo_models/ - rm PepNovo.20120423.zip - rm -rf /tmp/pepnovo -fi +# if [ ! -d test-data/pepnovo_models/ ]; then +# mkdir -p /tmp/pepnovo +# wget -nc http://proteomics.ucsd.edu/Software/PepNovo/PepNovo.20120423.zip +# unzip PepNovo.20120423.zip -d /tmp/pepnovo/ +# mv /tmp/pepnovo/Models test-data/pepnovo_models/ +# rm PepNovo.20120423.zip +# rm -rf /tmp/pepnovo +# fi ############################################################################### ## generate ctd files using the binaries in the conda package ############################################################################### @@ -170,6 +173,47 @@ ############################################################################### ## create script to create results for the tests and run it ############################################################################### +# parse data preparation calls from OpenMS sources for a tool with a given id +function prepare_test_data { +# id=$1 +# | egrep -i "$id\_.*[0-9]+(_prepare\"|_convert)?" + + OLD_OSW_PARAM=$(cat $OPENMSGIT/src/tests/topp/CMakeLists.txt |sed 's/#.*$//'| sed 's/^\s*//; s/\s*$//' |awk '{printf("%s@NEWLINE@", $0)}' | sed 's/)@NEWLINE@/)\n/g' | sed 's/@NEWLINE@/ /g' | grep OLD_OSW_PARAM | head -n 1 | sed 's/^[^"]\+//; s/)$//; s/"//g') + # TODO SiriusAdapter depends on online service which may timeout .. so keep disabled https://github.com/OpenMS/OpenMS/pull/5010 + cat $OPENMSGIT/src/tests/topp/CMakeLists.txt $OPENMSGIT/src/tests/topp/THIRDPARTY/third_party_tests.cmake | + sed "s/\${OLD_OSW_PARAM}/$OLD_OSW_PARAM/" | + grep -v "\.ini\.json" | + sed 's/.ini.json /ini /' | + sed 's/#.*$//'| + sed 's/^\s*//; s/\s*$//' | + grep -v "^$" | + awk '{printf("%s@NEWLINE@", $0)}' | + sed 's/)@NEWLINE@/)\n/g' | sed 's/@NEWLINE@/ /g' | + sed 's/degenerate_cases\///' | + egrep -v "WRITEINI|WRITECTD|INVALIDVALUE|DIFF" | + grep add_test | + egrep "TOPP|UTILS" | + sed 's@${DATA_DIR_SHARE}/@@g;'| + sed 's@${TMP_RIP_PATH}@./@g'| + sed 's@TOFCalibration_ref_masses @TOFCalibration_ref_masses.txt @g; s@TOFCalibration_const @TOFCalibration_const.csv @'| + sed 's/\("TOPP_SiriusAdapter_4".*\)-sirius:database all\(.*\)/\1-sirius:database pubchem\2/' | + while read line + do + test_id=$(echo "$line" | sed 's/add_test(//; s/"//g; s/)[^)]*$//; s/\${TOPP_BIN_PATH}\///g;s/\${DATA_DIR_TOPP}\///g; s#THIRDPARTY/##g' | cut -d" " -f1) + + if grep -lq "$test_id"'\".* PROPERTIES WILL_FAIL 1' $OPENMSGIT/src/tests/topp/CMakeLists.txt $OPENMSGIT/src/tests/topp/THIRDPARTY/third_party_tests.cmake; then + >&2 echo " skip failing "$test_id + continue + fi + + line=$(echo "$line" | sed 's/add_test("//; s/)[^)]*$//; s/\${TOPP_BIN_PATH}\///g;s/\${DATA_DIR_TOPP}\///g; s#THIRDPARTY/##g' | cut -d" " -f2-) + # line="$(fix_tmp_files $line)" + echo 'echo executing "'$test_id'"' + echo "$line > $test_id.stdout 2> $test_id.stderr" + echo "if [[ \"\$?\" -ne \"0\" ]]; then >&2 echo '$test_id failed'; >&2 echo -e \"stderr:\n\$(cat $test_id.stderr | sed 's/^/ /')\"; echo -e \"stdout:\n\$(cat $test_id.stdout)\";fi" + done +} + echo "Create test shell script" echo -n "" > prepare_test_data.sh @@ -180,31 +224,19 @@ echo 'export LUCIPHOR_BINARY="$(dirname $(realpath $(which luciphor2)))/luciphor2.jar"' >> prepare_test_data.sh echo 'export MARACLUSTER_BINARY="'"$OPENMSGIT"'/THIRDPARTY/Linux/64bit/MaRaCluster/maracluster"'>> prepare_test_data.sh -echo 'export MSFRAGGER_BINARY="/home/berntm/Downloads/MSFragger-20171106/MSFragger-20171106.jar"'>> prepare_test_data.sh +echo 'export MSFRAGGER_BINARY="/home/berntm/Downloads/MSFragger-3.5/MSFragger-3.5.jar"'>> prepare_test_data.sh echo 'export MSGFPLUS_BINARY="$(msgf_plus -get_jar_path)"' >> prepare_test_data.sh echo 'export MYRIMATCH_BINARY="myrimatch"'>> prepare_test_data.sh echo 'export NOVOR_BINARY="/home/berntm/Downloads/novor/lib/novor.jar"' >> prepare_test_data.sh -echo 'export OMSSA_BINARY="$(dirname $(realpath $(which omssacl)))/omssacl"'>> prepare_test_data.sh echo 'export PERCOLATOR_BINARY="percolator"'>> prepare_test_data.sh echo 'export SIRIUS_BINARY="$(which sirius)"' >> prepare_test_data.sh echo 'export SPECTRAST_BINARY="'"$OPENMSGIT"'/THIRDPARTY/Linux/64bit/SpectraST/spectrast"' >> prepare_test_data.sh echo 'export XTANDEM_BINARY="xtandem"' >> prepare_test_data.sh echo 'export THERMORAWFILEPARSER_BINARY="ThermoRawFileParser.exe"' >> prepare_test_data.sh +echo 'export SAGE_BINARY=sage' >> prepare_test_data.sh prepare_test_data >> prepare_test_data.sh #tmp_test_data.sh -## prepare_test_data > tmp_test_data.sh -## # remove calls not needed for the tools listed in any .list file -## echo LIST $LIST -## if [ ! -z "$LIST" ]; then -## REX=$(echo $LIST | sed 's/ /\n/g' | sed 's@.*/\([^/]\+\).xml$@\1@' | tr '\n' '|' | sed 's/|$//') -## else -## REX=".*" -## fi -## echo REX $REX -## cat tmp_test_data.sh | egrep "($REX)" >> prepare_test_data.sh -## rm tmp_test_data.sh - echo "Execute test shell script" chmod u+x prepare_test_data.sh cd ./test-data || exit @@ -234,14 +266,11 @@ for i in $(ls ctd/*ctd) do b=$(basename "$i" .ctd) - get_tests2 "$b" >> "$autotests" + ./get_tests.py --id "$b" --cmake "$OPENMSGIT"/src/tests/topp/CMakeLists.txt "$OPENMSGIT"/src/tests/topp/THIRDPARTY/third_party_tests.cmake >> "$autotests" + wc -l "$autotests" done echo "</macros>" >> "$autotests" -# echo "Create test data links" -# Breaks DecoyDatabase -# link_tmp_files - # tests for tools using output_prefix parameters can not be auto generated # hence we output the tests for manual curation in macros_test.xml # and remove them from the autotests @@ -255,6 +284,7 @@ # # not able to specify composite test data # -> SpectraSTSearchAdapter +echo "Discard some tests" if [[ ! -z "$1" ]]; then echo "" > macros_discarded_auto.xml for i in OpenSwathFileSplitter IDRipper MzMLSplitter SeedListGenerator MSFraggerAdapter MaRaClusterAdapter NovorAdapter SpectraSTSearchAdapter @@ -272,7 +302,7 @@ ## remove broken symlinks in test-data find test-data/ -xtype l -delete -if [ ! -z "$created" ]; then +if [[ "$created" == "yes" ]]; then echo "Removing temporary directory" rm -rf "$tmp" fi