Mercurial > repos > jjohnson > encyclopedia_library_to_blib
diff encyclopedia_library_to_blib.xml @ 0:058db6d8a1b3 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
| author | jjohnson |
|---|---|
| date | Fri, 19 Jun 2020 10:13:33 -0400 |
| parents | |
| children | 4850741d1dff |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/encyclopedia_library_to_blib.xml Fri Jun 19 10:13:33 2020 -0400 @@ -0,0 +1,40 @@ +<tool id="encyclopedia_library_to_blib" name="ConvertLibraryToBlib" version="@VERSION@.0" python_template_version="3.5"> + <description>Convert EncyclopeDIA Library to BLIB for Skyline</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <command detect_errors="exit_code"><![CDATA[ + EncyclopeDIA -convert -libtoblib + -i '$i' + -o '$output' + #if $istest == 'yes' + && sqlite3 -readonly '$output' 'SELECT distinct peptideSeq FROM RefSpectra;' > '$test_output' + #end if + ]]></command> + <inputs> + <param argument="-i" type="data" format="elib,dlib" label="Library: Chromatagram .ELIB or Spectrum .DLIB"/> + <param name="istest" type="hidden" value="no"/> + </inputs> + <outputs> + <data name="output" format="blib" label="${i.name} blib"/> + <data name="test_output" format="txt" > + <filter>istest == 'yes'</filter> + </data> + </outputs> + <tests> + <test> + <param name="i" ftype="dlib" value="PrositLib.dlib"/> + <param name="istest" value="yes"/> + <output name="test_output" ftype="txt"> + <assert_contents> + <has_text text="AGGVLHDDENLWSFGK"/> + </assert_contents> + </output> + </test> + </tests> + <help><![CDATA[ + Convert EncyclopeDIA Library to BLIB for Skyline. + ]]></help> + <expand macro="citations" /> +</tool>