changeset 7:dedfeaab569d draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit dd611a143e4e003a5fb085cdf93ae477cc5ea0b1-dirty"
author jjohnson
date Thu, 10 Sep 2020 19:04:03 +0000
parents 7003adde5668
children e3c67833efac
files macros.xml test-data/BCS_hela.elib test-data/BCS_hela_narrow_3_1.mzML test-data/BCS_hela_narrow_3_2.mzML test-data/BCS_hela_wide_500_900_1.mzML test-data/BCS_hela_wide_500_900_2.mzML test-data/PeptidesForProsit.csv test-data/PrositLib.csv test-data/PrositLib.dlib test-data/YeastProteinFasta5.fasta test-data/small_pan_human_library.dlib test-data/uniprot_human.fasta test-data/uniprot_tiny_human.fasta
diffstat 13 files changed, 6 insertions(+), 1011962 deletions(-) [+]
line wrap: on
line diff
--- a/macros.xml	Fri Aug 21 16:14:27 2020 -0400
+++ b/macros.xml	Thu Sep 10 19:04:03 2020 +0000
@@ -102,8 +102,12 @@
     </token>
 
     <xml name="target_fasta">
-        <param name="target_fasta" argument="-t" type="data" format="fasta" label="Target fasta database" optional="true"/> 
-        <param argument="-tp" type="boolean" truevalue="true" falsevalue="false" checked="false" label="target FASTA file contains peptides"/>
+        <param name="target_fasta" argument="-t" type="data" format="fasta" label="Target fasta database" optional="true"> 
+            <help>Optional - Only analyze this subset of the background fasta proteome</help>
+        </param>
+        <param argument="-tp" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Target FASTA file contains peptides">
+            <help>Rather than full proteins</help>
+        </param>
     </xml>
     <token name="@LINK_TARGET_FASTA@"><![CDATA[
     #if $target_fasta
Binary file test-data/BCS_hela.elib has changed
--- a/test-data/BCS_hela_narrow_3_1.mzML	Fri Aug 21 16:14:27 2020 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,113576 +0,0 @@
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-  <mzML xmlns="http://psi.hupo.org/ms/mzml" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psi.hupo.org/ms/mzml http://psidev.info/files/ms/mzML/xsd/mzML1.1.0.xsd" id="2018may16_hela_window_size_test_BCS_hela_narrow_3" version="1.1.0">
-    <cvList count="2">
-      <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="4.0.1" URI="http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo"/>
-      <cv id="UO" fullName="Unit Ontology" version="12:10:2011" URI="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/unit.obo"/>
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-        <cvParam cvRef="MS" accession="MS:1000580" name="MSn spectrum" value=""/>
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-      <sourceFileList count="2">
-        <sourceFile id="RAW1" name="2018may16_hela_window_size_test_BCS_hela_narrow_3.raw" location="file:///Z:\CCMSConversion\intermediate_files\ba2eb07be92c401a9cfe511c1fad9661_input">
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-        <sourceFile id="_x0032_018may16_hela_window_size_test_BCS_hela_narrow_3.mzML" name="2018may16_hela_window_size_test_BCS_hela_narrow_3.mzML" location="file:///">
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-        <cvParam cvRef="MS" accession="MS:1001911" name="Q Exactive" value=""/>
-        <cvParam cvRef="MS" accession="MS:1000529" name="instrument serial number" value="Exactive Series slot #1"/>
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-    <softwareList count="3">
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-      <software id="pwiz" version="3.0.9172">
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-      </software>
-      <software id="pwiz_3.0.9987" version="3.0.9987">
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-          <source order="1">
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-            <cvParam cvRef="MS" accession="MS:1000485" name="nanospray inlet" value=""/>
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-          <analyzer order="2">
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-          </analyzer>
-          <analyzer order="3">
-            <cvParam cvRef="MS" accession="MS:1000484" name="orbitrap" value=""/>
-          </analyzer>
-          <detector order="4">
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-          </detector>
-        </componentList>
-        <softwareRef ref="Xcalibur"/>
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-    <dataProcessingList count="2">
-      <dataProcessing id="pwiz_Reader_Thermo_conversion">
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-        <processingMethod order="1" softwareRef="pwiz">
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-          <userParam name="Thermo/Xcalibur peak picking"/>
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