# HG changeset patch
# User galaxyp
# Date 1612006727 0
# Node ID 047020d9012f0559537d6262566672c964f9cd4a
# Parent  59736982ab7b2001dada7580698d2cc7df70397a
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 173ee0ef8aa320d2f17433d6560fff05093d127e-dirty"

diff -r 59736982ab7b -r 047020d9012f PSMFeatureExtractor.xml
--- a/PSMFeatureExtractor.xml	Mon Dec 14 16:54:21 2020 +0000
+++ b/PSMFeatureExtractor.xml	Sat Jan 30 11:38:47 2021 +0000
@@ -1,7 +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]-->
-<tool id="PSMFeatureExtractor" name="PSMFeatureExtractor" version="@TOOL_VERSION@+galaxy1" profile="20.05">
+<tool id="PSMFeatureExtractor" name="PSMFeatureExtractor" version="@TOOL_VERSION@+galaxy2" profile="20.05">
   <description>Computes extra features for each input PSM.</description>
   <macros>
     <token name="@EXECUTABLE@">PSMFeatureExtractor</token>
@@ -34,7 +34,7 @@
 #if $in
 ${' '.join(["'in/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])}
 #else if $in_single
-'in/${re.sub("[^\w\-_]", "_", $in_single.element_identifier)}.$gxy2omsext($in_single.ext)' &&
+'in/${re.sub("[^\w\-_]", "_", $in_single.element_identifier)}.$gxy2omsext($in_single.ext)'
 #end if
 -out
 'out/output.${out_type}'
diff -r 59736982ab7b -r 047020d9012f macros_discarded_auto.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros_discarded_auto.xml	Sat Jan 30 11:38:47 2021 +0000
@@ -0,0 +1,378 @@
+
+<xml name="manutest_OpenSwathFileSplitter">
+<test expect_num_outputs="2">
+  <conditional name="adv_opts_cond">
+    <param name="adv_opts_selector" value="advanced"/>
+    <param name="force" value="false"/>
+    <param name="test" value="true"/>
+  </conditional>
+  <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
+  <output_collection name="outputDirectory" count=""/>
+  <output name="out_qc" file="OpenSwathFileSplitter_1.json" compare="sim_size" delta="5700" ftype="json"/>
+  <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_qc_FLAG"/>
+  <output name="ctd_out" ftype="xml">
+    <assert_contents>
+      <is_valid_xml/>
+    </assert_contents>
+  </output>
+</test></xml>
+<xml name="manutest_IDRipper">
+<test expect_num_outputs="1">
+      <conditional name="adv_opts_cond">
+        <param name="adv_opts_selector" value="advanced"/>
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </conditional>
+      <param name="in" value="IDRipper_1_input.idXML"/>
+      <output_collection name="out_path" count=""/>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test><test expect_num_outputs="1">
+      <conditional name="adv_opts_cond">
+        <param name="adv_opts_selector" value="advanced"/>
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </conditional>
+      <param name="in" value="IDRipper_2_input.idXML"/>
+      <output_collection name="out_path" count=""/>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test><test expect_num_outputs="1">
+      <conditional name="adv_opts_cond">
+        <param name="adv_opts_selector" value="advanced"/>
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </conditional>
+      <param name="in" value="IDRipper_3_output.idXML"/>
+      <output_collection name="out_path" count=""/>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test></xml>
+<xml name="manutest_MzMLSplitter">
+<test expect_num_outputs="1">
+      <conditional name="adv_opts_cond">
+        <param name="adv_opts_selector" value="advanced"/>
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </conditional>
+      <param name="in" value="FileFilter_1_input.mzML"/>
+      <output_collection name="out" count=""/>
+      <param name="parts" value="2"/>
+      <param name="size" value="0"/>
+      <param name="unit" value="MB"/>
+      <param name="no_chrom" value="false"/>
+      <param name="no_spec" value="false"/>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test><test expect_num_outputs="1">
+      <conditional name="adv_opts_cond">
+        <param name="adv_opts_selector" value="advanced"/>
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </conditional>
+      <param name="in" value="FileFilter_1_input.mzML"/>
+      <output_collection name="out" count=""/>
+      <param name="parts" value="1"/>
+      <param name="size" value="40"/>
+      <param name="unit" value="KB"/>
+      <param name="no_chrom" value="false"/>
+      <param name="no_spec" value="false"/>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test></xml>
+<xml name="manutest_MSFraggerAdapter">
+<test expect_num_outputs="3">
+      <conditional name="adv_opts_cond">
+        <param name="adv_opts_selector" value="advanced"/>
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </conditional>
+      <param name="java_heapmemory" value="2600"/>
+      <param name="in" value="spectra.mzML"/>
+      <output name="out" file="MSFraggerAdapter_7_out_tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
+      <output name="opt_out" file="MSFraggerAdapter_7_opt_out_tmp.pepXML" compare="sim_size" delta="5700" ftype="pepxml"/>
+      <param name="database" value="proteins.fasta"/>
+      <section name="tolerance">
+        <param name="precursor_mass_tolerance" value="20.0"/>
+        <param name="precursor_mass_unit" value="ppm"/>
+        <param name="precursor_true_tolerance" value="0.0"/>
+        <param name="precursor_true_unit" value="ppm"/>
+        <param name="fragment_mass_tolerance" value="20.0"/>
+        <param name="fragment_mass_unit" value="ppm"/>
+        <param name="isotope_error" value="0"/>
+      </section>
+      <section name="digest">
+        <param name="search_enzyme_name" value="Trypsin"/>
+        <param name="search_enzyme_cutafter" value="KR"/>
+        <param name="search_enzyme_nocutbefore" value="P"/>
+        <param name="num_enzyme_termini" value="semi"/>
+        <param name="allowed_missed_cleavage" value="2"/>
+        <param name="min_length" value="7"/>
+        <param name="max_length" value="64"/>
+        <param name="mass_range_min" value="500.0"/>
+        <param name="mass_range_max" value="5000.0"/>
+      </section>
+      <section name="varmod">
+        <param name="clip_nterm_m" value="false"/>
+        <param name="masses" value=""/>
+        <param name="syntaxes" value=""/>
+        <param name="enable_common" value="true"/>
+        <param name="not_allow_multiple_variable_mods_on_residue" value="false"/>
+        <param name="max_variable_mods_per_mod" value="2"/>
+        <param name="max_variable_mods_combinations" value="5000"/>
+      </section>
+      <section name="spectrum">
+        <param name="minimum_peaks" value="10"/>
+        <param name="use_topn_peaks" value="50"/>
+        <param name="minimum_ratio" value="0.0"/>
+        <param name="clear_mz_range_min" value="0.0"/>
+        <param name="clear_mz_range_max" value="0.0"/>
+        <param name="max_fragment_charge" value="2"/>
+        <param name="override_charge" value="false"/>
+        <param name="precursor_charge_min" value="1"/>
+        <param name="precursor_charge_max" value="4"/>
+      </section>
+      <section name="search">
+        <param name="track_zero_topn" value="0"/>
+        <param name="zero_bin_accept_expect" value="0.0"/>
+        <param name="zero_bin_mult_expect" value="1.0"/>
+        <param name="add_topn_complementary" value="0"/>
+        <param name="min_fragments_modeling" value="3"/>
+        <param name="min_matched_fragments" value="4"/>
+        <param name="output_report_topn" value="1"/>
+        <param name="output_max_expect" value="50.0"/>
+      </section>
+      <section name="statmod">
+        <param name="add_cterm_peptide" value="0.0"/>
+        <param name="add_nterm_peptide" value="0.0"/>
+        <param name="add_cterm_protein" value="0.0"/>
+        <param name="add_nterm_protein" value="0.0"/>
+        <param name="add_G_glycine" value="0.0"/>
+        <param name="add_A_alanine" value="0.0"/>
+        <param name="add_S_serine" value="0.0"/>
+        <param name="add_P_proline" value="0.0"/>
+        <param name="add_V_valine" value="0.0"/>
+        <param name="add_T_threonine" value="0.0"/>
+        <param name="add_C_cysteine" value="57.021464"/>
+        <param name="add_L_leucine" value="0.0"/>
+        <param name="add_I_isoleucine" value="0.0"/>
+        <param name="add_N_asparagine" value="0.0"/>
+        <param name="add_D_aspartic_acid" value="0.0"/>
+        <param name="add_Q_glutamine" value="0.0"/>
+        <param name="add_K_lysine" value="0.0"/>
+        <param name="add_E_glutamic_acid" value="0.0"/>
+        <param name="add_M_methionine" value="0.0"/>
+        <param name="add_H_histidine" value="0.0"/>
+        <param name="add_F_phenylalanine" value="0.0"/>
+        <param name="add_R_arginine" value="0.0"/>
+        <param name="add_Y_tyrosine" value="0.0"/>
+        <param name="add_W_tryptophan" value="0.0"/>
+      </section>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,opt_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test><test expect_num_outputs="2">
+      <conditional name="adv_opts_cond">
+        <param name="adv_opts_selector" value="advanced"/>
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </conditional>
+      <param name="java_heapmemory" value="2600"/>
+      <param name="in" value="spectra_comet.mzML"/>
+      <output name="out" file="MSFraggerAdapter_8_out_tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
+      <param name="database" value="proteins.fasta"/>
+      <section name="tolerance">
+        <param name="precursor_mass_tolerance" value="20.0"/>
+        <param name="precursor_mass_unit" value="ppm"/>
+        <param name="precursor_true_tolerance" value="0.0"/>
+        <param name="precursor_true_unit" value="ppm"/>
+        <param name="fragment_mass_tolerance" value="20.0"/>
+        <param name="fragment_mass_unit" value="ppm"/>
+        <param name="isotope_error" value="0"/>
+      </section>
+      <section name="digest">
+        <param name="search_enzyme_name" value="Trypsin"/>
+        <param name="search_enzyme_cutafter" value="KR"/>
+        <param name="search_enzyme_nocutbefore" value="P"/>
+        <param name="num_enzyme_termini" value="semi"/>
+        <param name="allowed_missed_cleavage" value="2"/>
+        <param name="min_length" value="7"/>
+        <param name="max_length" value="64"/>
+        <param name="mass_range_min" value="500.0"/>
+        <param name="mass_range_max" value="5000.0"/>
+      </section>
+      <section name="varmod">
+        <param name="clip_nterm_m" value="false"/>
+        <param name="masses" value=""/>
+        <param name="syntaxes" value=""/>
+        <param name="enable_common" value="true"/>
+        <param name="not_allow_multiple_variable_mods_on_residue" value="false"/>
+        <param name="max_variable_mods_per_mod" value="2"/>
+        <param name="max_variable_mods_combinations" value="5000"/>
+      </section>
+      <section name="spectrum">
+        <param name="minimum_peaks" value="10"/>
+        <param name="use_topn_peaks" value="50"/>
+        <param name="minimum_ratio" value="0.0"/>
+        <param name="clear_mz_range_min" value="0.0"/>
+        <param name="clear_mz_range_max" value="0.0"/>
+        <param name="max_fragment_charge" value="2"/>
+        <param name="override_charge" value="false"/>
+        <param name="precursor_charge_min" value="1"/>
+        <param name="precursor_charge_max" value="4"/>
+      </section>
+      <section name="search">
+        <param name="track_zero_topn" value="0"/>
+        <param name="zero_bin_accept_expect" value="0.0"/>
+        <param name="zero_bin_mult_expect" value="1.0"/>
+        <param name="add_topn_complementary" value="0"/>
+        <param name="min_fragments_modeling" value="3"/>
+        <param name="min_matched_fragments" value="4"/>
+        <param name="output_report_topn" value="1"/>
+        <param name="output_max_expect" value="50.0"/>
+      </section>
+      <section name="statmod">
+        <param name="add_cterm_peptide" value="0.0"/>
+        <param name="add_nterm_peptide" value="0.0"/>
+        <param name="add_cterm_protein" value="0.0"/>
+        <param name="add_nterm_protein" value="0.0"/>
+        <param name="add_G_glycine" value="0.0"/>
+        <param name="add_A_alanine" value="0.0"/>
+        <param name="add_S_serine" value="0.0"/>
+        <param name="add_P_proline" value="0.0"/>
+        <param name="add_V_valine" value="0.0"/>
+        <param name="add_T_threonine" value="0.0"/>
+        <param name="add_C_cysteine" value="57.021464"/>
+        <param name="add_L_leucine" value="0.0"/>
+        <param name="add_I_isoleucine" value="0.0"/>
+        <param name="add_N_asparagine" value="0.0"/>
+        <param name="add_D_aspartic_acid" value="0.0"/>
+        <param name="add_Q_glutamine" value="0.0"/>
+        <param name="add_K_lysine" value="0.0"/>
+        <param name="add_E_glutamic_acid" value="0.0"/>
+        <param name="add_M_methionine" value="0.0"/>
+        <param name="add_H_histidine" value="0.0"/>
+        <param name="add_F_phenylalanine" value="0.0"/>
+        <param name="add_R_arginine" value="0.0"/>
+        <param name="add_Y_tyrosine" value="0.0"/>
+        <param name="add_W_tryptophan" value="0.0"/>
+      </section>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test></xml>
+<xml name="manutest_MaRaClusterAdapter">
+<test expect_num_outputs="2">
+      <conditional name="adv_opts_cond">
+        <param name="adv_opts_selector" value="advanced"/>
+        <param name="verbose" value="2"/>
+        <param name="precursor_tolerance" value="20.0"/>
+        <param name="precursor_tolerance_units" value="ppm"/>
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </conditional>
+      <param name="in" value="MaRaClusterAdapter_1_in_1.mzML,MaRaClusterAdapter_1_in_2.mzML"/>
+      <param name="id_in" value="MaRaClusterAdapter_1_in_3.idXML"/>
+      <output name="out" file="MaRaClusterAdapter_2_out_1.tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
+      <param name="pcut" value="-10.0"/>
+      <param name="min_cluster_size" value="1"/>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test></xml>
+<xml name="manutest_NovorAdapter">
+<test expect_num_outputs="2">
+      <conditional name="adv_opts_cond">
+        <param name="adv_opts_selector" value="advanced"/>
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </conditional>
+      <param name="in" value="NovorAdapter_in.mzML"/>
+      <output name="out" file="NovorAdapter_1_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
+      <param name="enzyme" value="Trypsin"/>
+      <param name="fragmentation" value="CID"/>
+      <param name="massAnalyzer" value="Trap"/>
+      <param name="fragment_mass_tolerance" value="0.5"/>
+      <param name="precursor_mass_tolerance" value="15.0"/>
+      <param name="precursor_error_units" value="ppm"/>
+      <param name="variable_modifications" value="Acetyl (K)"/>
+      <param name="fixed_modifications" value="Carbamidomethyl (C)"/>
+      <param name="forbiddenResidues" value="I"/>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test></xml>
+<xml name="manutest_SpectraSTSearchAdapter">
+<test expect_num_outputs="2">
+      <conditional name="adv_opts_cond">
+        <param name="adv_opts_selector" value="advanced"/>
+        <param name="use_isotopically_averaged_mass" value="false"/>
+        <param name="use_all_charge_states" value="false"/>
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </conditional>
+      <param name="spectra_files" value="SpectrastAdapter_1_hack.mzML"/>
+      <param name="output_files_type" value="pep.xml"/>
+      <output_collection name="output_files" count="1"/>
+      <param name="library_file" value="testLib.splib" ftype="splib"/>
+      <param name="sequence_database_type" value="AA"/>
+      <param name="precursor_mz_tolerance" value="3.0"/>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test><test expect_num_outputs="2">
+      <conditional name="adv_opts_cond">
+        <param name="adv_opts_selector" value="advanced"/>
+        <param name="use_isotopically_averaged_mass" value="false"/>
+        <param name="use_all_charge_states" value="false"/>
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </conditional>
+      <param name="spectra_files" value="SpectrastAdapter_1_hack.mzML"/>
+      <param name="output_files_type" value="tsv"/>
+      <output_collection name="output_files" count="1"/>
+      <param name="library_file" value="testLib.splib" ftype="splib"/>
+      <param name="sequence_database_type" value="AA"/>
+      <param name="precursor_mz_tolerance" value="3.0"/>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test></xml>
diff -r 59736982ab7b -r 047020d9012f test-data/spectrast.log
--- a/test-data/spectrast.log	Mon Dec 14 16:54:21 2020 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,22 +0,0 @@
-START: (Sun Dec 13 17:22:43 2020) /tmp/openms-stuff//OpenMS2.6.0-git/THIRDPARTY/Linux/64bit/SpectraST/spectrast -s -sM3 -sLtestLib.splib -sP! -sA! -sz! -sEpepXML -sO/tmp SpectrastAdapter_1_hack.mzML 
-GENERAL: File offset size is 8 bytes. Big library supported.
-GENERAL: Pointer size is 8 bytes.
-MZXML SEARCH: Sorted query spectra in "SpectrastAdapter_1_hack.mzML" by precursor m/z
-MZXML SEARCH: Searched "SpectrastAdapter_1_hack.mzML" (Max 3 scans; 3 searched, 0 likely good; 0 failed filter; 0 missing; 0 MS1)
-MZXML SEARCH: Searched 1 files total (Max 3 scans; 3 searched, 0 likely good; 0 failed filter; 0 missing; 0 MS1)
-SEARCH STATS: Breakdown: +1 = 0 ; +2 = 0 ; +3 = 0 ; +4 = 0 ; +5 = 0 ; 
-PERFORMANCE: Total Run Time = 0 seconds. Total Number of Searches Performed = 3. Run Time per Search = 0 seconds..
-
-END: (Sun Dec 13 17:22:43 2020) /tmp/openms-stuff//OpenMS2.6.0-git/THIRDPARTY/Linux/64bit/SpectraST/spectrast -s -sM3 -sLtestLib.splib -sP! -sA! -sz! -sEpepXML -sO/tmp SpectrastAdapter_1_hack.mzML 
-==========
-START: (Sun Dec 13 17:22:43 2020) /tmp/openms-stuff//OpenMS2.6.0-git/THIRDPARTY/Linux/64bit/SpectraST/spectrast -s -sM3 -sLtestLib.splib -sP! -sA! -sz! -sEtsv -sO/tmp SpectrastAdapter_1_hack.mzML 
-GENERAL: File offset size is 8 bytes. Big library supported.
-GENERAL: Pointer size is 8 bytes.
-MZXML SEARCH: Sorted query spectra in "SpectrastAdapter_1_hack.mzML" by precursor m/z
-MZXML SEARCH: Searched "SpectrastAdapter_1_hack.mzML" (Max 3 scans; 3 searched, 0 likely good; 0 failed filter; 0 missing; 0 MS1)
-MZXML SEARCH: Searched 1 files total (Max 3 scans; 3 searched, 0 likely good; 0 failed filter; 0 missing; 0 MS1)
-SEARCH STATS: Breakdown: +1 = 0 ; +2 = 0 ; +3 = 0 ; +4 = 0 ; +5 = 0 ; 
-PERFORMANCE: Total Run Time = 1 seconds. Total Number of Searches Performed = 3. Run Time per Search = 0.333333 seconds..
-
-END: (Sun Dec 13 17:22:44 2020) /tmp/openms-stuff//OpenMS2.6.0-git/THIRDPARTY/Linux/64bit/SpectraST/spectrast -s -sM3 -sLtestLib.splib -sP! -sA! -sz! -sEtsv -sO/tmp SpectrastAdapter_1_hack.mzML 
-==========