Mercurial > repos > galaxyp > mz_to_sqlite

changeset 3:728d459bafe8 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite commit 1acf110c8836bf573d241a8fd33c842da369e76c"
author galaxyp
date Mon, 29 Jun 2020 17:06:00 -0400
parents 1320693cbf1e
children f5c632894818
files mz_to_sqlite.xml
diffstat 1 files changed, 11 insertions(+), 12 deletions(-) [+]
line wrap: on
line diff
--- a/mz_to_sqlite.xml	Mon Feb 11 17:30:46 2019 -0500
+++ b/mz_to_sqlite.xml	Mon Jun 29 17:06:00 2020 -0400
@@ -1,13 +1,13 @@
-<tool id="mz_to_sqlite" name="mz to sqlite" version="2.0.2">
+<tool id="mz_to_sqlite" name="mz to sqlite" version="2.0.4">
     <description>Extract mzIdentML and associated proteomics datasets into a SQLite DB</description>
     <requirements>
-      <requirement type="package" version="2.0.2">mztosqlite</requirement>
+        <requirement type="package" version="2.0.4">mztosqlite</requirement>
     </requirements>
-   <stdio>
-       <exit_code range="1:"  level="fatal" description="Error Running mz_to_sqlite" />
-   </stdio>
+    <stdio>
+        <exit_code range="1:" level="fatal" description="Error Running mz_to_sqlite" />
+    </stdio>
     <command>
-<![CDATA[
+        <![CDATA[
 mz_to_sqlite -Xms1g -Xmx6g 
      -numthreads "\${GALAXY_SLOTS:-4}"
      -dbname 'sqlite.db'
@@ -28,13 +28,12 @@
 ]]>
     </command>
     <inputs>
-        <param name="mzinput" type="data" format="mzid" label="Proteomics Identification files"/>
-        <param name="scanfiles" type="data" format="mzml,mgf" multiple="true" optional="true" label="Proteomics Spectrum files"/>
-        <param name="searchdbs" type="data" format="fasta,uniprotxml" multiple="true" optional="true" label="Proteomics Search Database Fasta"
-               help="These can provide sequences and length for proteins if not already present in the mzIdentML input"/>
+        <param name="mzinput" type="data" format="mzid" label="Proteomics Identification files" />
+        <param name="scanfiles" type="data" format="mgf" multiple="true" optional="true" label="Proteomics Spectrum files" />
+        <param name="searchdbs" type="data" format="fasta,uniprotxml" multiple="true" optional="true" label="Proteomics Search Database Fasta" help="These can provide sequences and length for proteins if not already present in the mzIdentML input" />
     </inputs>
     <outputs>
-        <data format="mz.sqlite" name="sqlite_db" label="${tool.name} on ${on_string}" from_work_dir="sqlite.db"/>
+        <data format="mz.sqlite" name="sqlite_db" label="${tool.name} on ${on_string}" from_work_dir="sqlite.db" />
     </outputs>
     <tests>
         <test>
@@ -45,7 +44,7 @@
         </test>
     </tests>
     <help>
-<![CDATA[
+        <![CDATA[
 ** mz_to_sqlite  converts proteomics file formats to a SQLite database**
 
 ]]>