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changeset 0:4e23dcad9087 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit d390af4450c890f34bfb02a5c1feaaa10b015411-dirty
author jjohnson
date Mon, 14 May 2018 14:48:42 -0400
parents
children 390a3c4a7f6b
files macros.xml spectrast_import.xml test-data/test.ms2
diffstat 3 files changed, 721 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Mon May 14 14:48:42 2018 -0400
@@ -0,0 +1,15 @@
+<macros>
+    <token name="@VERSION@">5.0.0</token>
+    <xml name="requirements">
+        <requirements>
+        <requirement type="package" version="5.0.0">tpp</requirement>
+            <yield/>
+        </requirements>
+    </xml>
+    <xml name="citations">
+        <citations>
+            <citation type="doi">10.1002/pmic.200600625</citation>
+            <yield />
+        </citations>
+    </xml>
+</macros>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/spectrast_import.xml	Mon May 14 14:48:42 2018 -0400
@@ -0,0 +1,44 @@
+<tool id="spectrast_import" name="SpectraST Import" version="@VERSION@.0">
+    <description>Spectral Library</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+        ## Symlink dataset to name with recognized ext
+        #import re
+        #set $ext = '.' + str($input.extension)
+        #set $input_name = $re.sub('[.](ms2|msp|hlf)$','',$input.display_name.split('/')[-1]) + $ext
+        ln -s '$input' '$input_name' &&
+        mkdir -p '$output.files_path' &&
+        spectrast -cN'${output.files_path}/library' '$input_name' | tee '$output'
+    ]]></command>
+    <inputs>
+        <param name="input" type="data" format="ms2,msp,hlf" label="Spectral library ms2, msp, or hlf" 
+             help="BiblioSpec .ms2,  NIST .msp,  or X!Hunter .hlf"/>
+    </inputs>
+    <outputs>
+        <data name="output" format="splib"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" ftype="ms2" value="test.ms2"/>
+            <output name="output">
+                <assert_contents>
+                    <has_text_matching expression="Total number of spectra in library: 1" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+**What it does**
+
+Imports a spectral library from the following formats:
+
+    NIST (National Institute of Standards and Technology)'s .msp format 
+    X!Hunter's .hlf format 
+    BiblioSpec's .ms2 format 
+
+    ]]></help>
+    <expand macro="citations" />
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test.ms2	Mon May 14 14:48:42 2018 -0400
@@ -0,0 +1,662 @@
+H	CreationDate	Mon May  7 19:27:23 2018
+H	Extractor	BlibToMs2
+H	Comment	Library	/panfs/roc/groups/7/galaxy/galaxy/tmp/bibliospec/msgf.blib
+S	1	1	784.865
+Z	2	1550.64
+D	seq	FKWNGTDTNSAAEK
+D	modified seq	FKWNGTDTNSAAEK
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+1459.69	232.7
+1472.73	339.1
+1505.74	292.4
+1565.08	294.4