--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CruxAdapter.xml	Wed Sep 09 12:57:00 2020 +0000
@@ -0,0 +1,158 @@
+<?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: [Identification]-->
+<tool id="CruxAdapter" name="CruxAdapter" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
+  <description>Identifies MS/MS spectra using Crux.</description>
+  <macros>
+    <token name="@EXECUTABLE@">CruxAdapter</token>
+    <import>macros.xml</import>
+    <import>macros_autotest.xml</import>
+    <import>macros_test.xml</import>
+  </macros>
+  <expand macro="requirements"/>
+  <expand macro="stdio"/>
+  <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
+@EXT_FOO@
+#import re
+
+## Preprocessing
+mkdir in &&
+ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+mkdir out &&
+mkdir database &&
+ln -s '$database' 'database/${re.sub("[^\w\-_]", "_", $database.element_identifier)}.$gxy2omsext($database.ext)' &&
+
+## Main program call
+
+set -o pipefail &&
+@EXECUTABLE@ -write_ctd ./ &&
+python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
+@EXECUTABLE@ -ini @EXECUTABLE@.ctd
+-in
+'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
+-out
+'out/output.${gxy2omsext("idxml")}'
+-database
+'database/${re.sub("[^\w\-_]", "_", $database.element_identifier)}.$gxy2omsext($database.ext)'
+
+## Postprocessing
+&& mv 'out/output.${gxy2omsext("idxml")}' '$out'
+#if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
+  && mv '@EXECUTABLE@.ctd' '$ctd_out'
+#end if]]></command>
+  <configfiles>
+    <inputs name="args_json" data_style="paths"/>
+    <configfile name="hardcoded_json"><![CDATA[{"crux_executable": "crux", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
+  </configfiles>
+  <inputs>
+    <param name="in" argument="-in" type="data" format="mzml" optional="false" label="Input file" help=" select mzml data sets(s)"/>
+    <param name="database" argument="-database" type="data" format="fasta" optional="false" label="FASTA file" help=" select fasta data sets(s)"/>
+    <param name="extra_index_args" argument="-extra_index_args" type="text" optional="true" value="" label="Extra arguments to be passed to tide-index" help="">
+      <expand macro="list_string_san"/>
+    </param>
+    <param name="extra_search_args" argument="-extra_search_args" type="text" optional="true" value="" label="Extra arguments to be passed to tide-search" help="">
+      <expand macro="list_string_san"/>
+    </param>
+    <param name="extra_percolator_args" argument="-extra_percolator_args" type="text" optional="true" value="" label="Extra arguments to be passed to percolato" help="">
+      <expand macro="list_string_san"/>
+    </param>
+    <param name="precursor_mass_tolerance" argument="-precursor_mass_tolerance" type="float" optional="true" value="10.0" label="Precursor monoisotopic mass tolerance (Crux parameter: peptide_mass_tolerance)" help=""/>
+    <param name="precursor_mass_units" argument="-precursor_mass_units" display="radio" type="select" optional="false" label="Unit of precursor mass tolerance (amu, m/z or ppm)" help="">
+      <option value="mass">mass</option>
+      <option value="mz">mz</option>
+      <option value="ppm" selected="true">ppm</option>
+      <expand macro="list_string_san"/>
+    </param>
+    <param name="fragment_bin_offset" argument="-fragment_bin_offset" type="float" optional="true" value="0.0" label="In the discretization of the m/z axes of the observed and theoretical spectra, this parameter specifies the location of the left edge of the first bin, relative to mass = 0" help="(i.e., mz-bin-offset = 0.xx means the left edge of the first bin will be located at +0.xx Da)"/>
+    <param name="fragment_bin_width" argument="-fragment_bin_width" type="float" optional="true" value="0.02" label="Before calculation of the XCorr score, the m/z axes of the observed and theoretical spectra are discretized" help="This parameter specifies the size of each bin. The exact formula for computing the discretized m/z value is floor((x/mz-bin-width) + 1.0 - mz-bin-offset), where x is the observed m/z value. For low resolution ion trap ms/ms data 1.0005079 and for high resolution ms/ms 0.02 is recommended"/>
+    <param name="isotope_error" argument="-isotope_error" type="text" optional="true" value="" label="List of positive, non-zero integers" help="">
+      <expand macro="list_string_san"/>
+    </param>
+    <param name="run_percolator" argument="-run_percolator" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Whether to run percolator after tide-search" help=""/>
+    <param name="enzyme" argument="-enzyme" type="select" optional="false" label="The enzyme used for peptide digestion" help="">
+      <option value="custom-enzyme">custom-enzyme</option>
+      <option value="glu-c">glu-c</option>
+      <option value="pepsin-a">pepsin-a</option>
+      <option value="cyanogen-bromide">cyanogen-bromide</option>
+      <option value="clostripain">clostripain</option>
+      <option value="elastase-trypsin-chymotrypsin">elastase-trypsin-chymotrypsin</option>
+      <option value="arg-c">arg-c</option>
+      <option value="asp-n">asp-n</option>
+      <option value="no-enzyme">no-enzyme</option>
+      <option value="iodosobenzoate">iodosobenzoate</option>
+      <option value="staph-protease">staph-protease</option>
+      <option value="proline-endopeptidase">proline-endopeptidase</option>
+      <option value="elastase">elastase</option>
+      <option value="chymotrypsin">chymotrypsin</option>
+      <option value="lys-c">lys-c</option>
+      <option value="lys-n">lys-n</option>
+      <option value="trypsin/p">trypsin/p</option>
+      <option value="trypsin" selected="true">trypsin</option>
+      <expand macro="list_string_san"/>
+    </param>
+    <param name="digestion" argument="-digestion" display="radio" type="select" optional="false" label="Full, partial or non specific digestion" help="">
+      <option value="full-digest" selected="true">full-digest</option>
+      <option value="partial-digest">partial-digest</option>
+      <option value="non-specific-digest">non-specific-digest</option>
+      <expand macro="list_string_san"/>
+    </param>
+    <param name="allowed_missed_cleavages" argument="-allowed_missed_cleavages" type="integer" optional="true" value="0" label="Number of possible cleavage sites missed by the enzyme, maximum value is 5; for enzyme search" help=""/>
+    <param name="decoy_format" argument="-decoy-format" display="radio" type="select" optional="false" label="Decoy generation method either by reversing the sequence or shuffling it" help="">
+      <option value="none">none</option>
+      <option value="shuffle" selected="true">shuffle</option>
+      <option value="peptide-reverse">peptide-reverse</option>
+      <option value="protein-reverse">protein-reverse</option>
+      <expand macro="list_string_san"/>
+    </param>
+    <param name="keep_terminal_aminos" argument="-keep-terminal-aminos" display="radio" type="select" optional="false" label="Whether to keep N and C terminal in place or also shuffled / reversed" help="">
+      <option value="N">N</option>
+      <option value="C">C</option>
+      <option value="NC" selected="true">NC</option>
+      <option value="none">none</option>
+      <expand macro="list_string_san"/>
+    </param>
+    <param name="cterm_modifications" argument="-cterm_modifications" type="text" optional="true" value="" label="Specifies C-terminal static and variable mass modifications on peptides" help="Specify a comma-separated list of C-terminal modification sequences of the form: X+21.9819 Default = &lt;empty&gt;">
+      <expand macro="list_string_san"/>
+    </param>
+    <param name="nterm_modifications" argument="-nterm_modifications" type="text" optional="true" value="" label="Specifies N-terminal static and variable mass modifications on peptides" help="Specify a comma-separated list of N-terminal modification sequences of the form: 1E-18.0106,C-17.0265 Default = &lt;empty&gt;">
+      <expand macro="list_string_san"/>
+    </param>
+    <param name="modifications" argument="-modifications" type="text" optional="true" value="" label="Expression for static and variable mass modifications to include" help="Specify a comma-separated list of modification sequences of the form: C+57.02146,2M+15.9949,1STY+79.966331,... Default = C+57.02146">
+      <expand macro="list_string_san"/>
+    </param>
+    <param name="test_fdr" argument="-test_fdr" type="float" optional="true" value="0.01" label="False discovery rate threshold used in selecting hyperparameters during internal cross-validation and for reporting the final results" help=""/>
+    <param name="train_fdr" argument="-train_fdr" type="float" optional="true" value="0.01" label="False discovery rate threshold to define positive examples in training" help=""/>
+    <expand macro="adv_opts_macro">
+      <param name="custom_enzyme" argument="-custom_enzyme" type="text" optional="true" value="" label="Specify rules for in silico digestion of protein sequences" help="Overrides the enzyme option. Two lists of residues are given enclosed in square brackets or curly braces and separated by a |. The first list contains residues required/prohibited before the cleavage site and the second list is residues after the cleavage site.  ">
+        <expand macro="list_string_san"/>
+      </param>
+      <param name="decoy_prefix" argument="-decoy_prefix" type="text" optional="true" value="decoy_" label="Specifies the prefix of the protein names that indicate a decoy" help="">
+        <expand macro="list_string_san"/>
+      </param>
+      <param name="deisotope" argument="-deisotope" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Deisotope spectra before searching" help=""/>
+      <param name="report_decoys" argument="-report_decoys" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Include decoys in the final reported dataset" help=""/>
+      <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/>
+      <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+        <expand macro="list_string_san"/>
+      </param>
+    </expand>
+    <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true">
+      <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
+    </param>
+  </inputs>
+  <outputs>
+    <data name="out" label="${tool.name} on ${on_string}: out" format="idxml"/>
+    <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
+      <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
+    </data>
+  </outputs>
+  <tests>
+    <expand macro="autotest_CruxAdapter"/>
+    <expand macro="manutest_CruxAdapter"/>
+  </tests>
+  <help><![CDATA[Identifies MS/MS spectra using Crux.
+
+
+For more information, visit http://www.openms.de/documentation/TOPP_CruxAdapter.html]]></help>
+  <expand macro="references"/>
+</tool>