Mercurial > repos > jjohnson > encyclopedia_encyclopedia

comparison encyclopedia_encyclopedia.xml @ 5:aeda6093dd40 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 880d327a6dce00616a0b0b58bcabcea7b58358cc"
author jjohnson
date Wed, 19 Aug 2020 08:35:54 -0400
parents e191adb34d04
children 61692bb2c78f
comparison
equal deleted inserted replaced
4:e191adb34d04 5:aeda6093dd40
27 <expand macro="lib_input" optional="false" libhelp="Chromatogram elib from SearchToLib on pooled samples"/> 27 <expand macro="lib_input" optional="false" libhelp="Chromatogram elib from SearchToLib on pooled samples"/>
28 <expand macro="options_section"/> 28 <expand macro="options_section"/>
29 <param name="select_outputs" type="select" label="Select outputs" multiple="true"> 29 <param name="select_outputs" type="select" label="Select outputs" multiple="true">
30 <option value="log" selected="true">log</option> 30 <option value="log" selected="true">log</option>
31 <option value="elib" selected="true">elib</option> 31 <option value="elib" selected="true">elib</option>
32 <option value="first_delta_rt_pdf" selected="true">encyclopedia.txt.first.delta_rt.pdf</option> 32 <option value="first_delta_rt_pdf" selected="false">encyclopedia.txt.first.delta_rt.pdf</option>
33 <option value="first_rt_fit_pdf" selected="true">encyclopedia.txt.first.rt_fit.pdf</option> 33 <option value="first_rt_fit_pdf" selected="false">encyclopedia.txt.first.rt_fit.pdf</option>
34 <option value="first_rt_fit_txt" selected="true">encyclopedia.txt.first.rt_fit.txt</option> 34 <option value="first_rt_fit_txt" selected="false">encyclopedia.txt.first.rt_fit.txt</option>
35 <option value="final_delta_rt_pdf" selected="true">encyclopedia.txt.final.delta_rt.pdf</option> 35 <option value="final_delta_rt_pdf" selected="false">encyclopedia.txt.final.delta_rt.pdf</option>
36 <option value="final_rt_fit_pdf" selected="true">encyclopedia.txt.final.rt_fit.pdf</option> 36 <option value="final_rt_fit_pdf" selected="false">encyclopedia.txt.final.rt_fit.pdf</option>
37 <option value="final_rt_fit_txt" selected="true">encyclopedia.txt.final.rt_fit.txt</option> 37 <option value="final_rt_fit_txt" selected="false">encyclopedia.txt.final.rt_fit.txt</option>
38 <option value="features" selected="true">features.txt</option> 38 <option value="features" selected="true">features.txt</option>
39 <option value="encyclopedia" selected="true">encyclopedia.txt</option> 39 <option value="encyclopedia" selected="true">encyclopedia.txt</option>
40 <option value="encyclopedia_decoy" selected="true">encyclopedia.decoy.txt</option> 40 <option value="encyclopedia_decoy" selected="false">encyclopedia.decoy.txt</option>
41 </param> 41 </param>
42 </inputs> 42 </inputs>
43 <outputs> 43 <outputs>
44 <data name="log" format="txt" label="${tool.name} ${on_string} log" from_work_dir="gxpedia.log"> 44 <data name="log" format="txt" label="${tool.name} ${on_string} log" from_work_dir="gxpedia.log">
45 <filter>'log' in select_outputs</filter> 45 <filter>'log' in select_outputs</filter>
88 <actions> 88 <actions>
89 <action name="column_names" type="metadata" default="PSMId,score,q-value,posterior_error_prob,peptide,proteinIds" /> 89 <action name="column_names" type="metadata" default="PSMId,score,q-value,posterior_error_prob,peptide,proteinIds" />
90 </actions> 90 </actions>
91 </data> 91 </data>
92 </outputs> 92 </outputs>
93 <tests>
94 <test>
95 <param name="scan_input" ftype="mzml" value="BCS_hela_wide_500_900_1.mzML"/>
96 <param name="library" ftype="elib" value="BCS_hela.elib"/>
97 <param name="fasta" ftype="fasta" value="uniprot_human.fasta"/>
98 <output name="features" ftype="tabular">
99 <assert_contents>
100 <has_text text="ESYDDVSSFR"/>
101 </assert_contents>
102 </output>
103 <output name="encyclopedia" ftype="tabular">
104 <assert_contents>
105 <has_text text="ESYDDVSSFR"/>
106 </assert_contents>
107 </output>
108 </test>
109 </tests>
110
93 <help><![CDATA[ 111 <help><![CDATA[
94 **EncyclopeDIA** 112 **EncyclopeDIA**
95 113
96 @ENCYCLOPEDIA_WIKI@ 114 @ENCYCLOPEDIA_WIKI@
97 115
110 128
111 **Outputs** 129 **Outputs**
112 130
113 - A log file 131 - A log file
114 - The identified features in tabular format 132 - The identified features in tabular format
133 - The identified proteins in tabular format
115 134
116 ]]></help> 135 ]]></help>
117 <expand macro="citations" /> 136 <expand macro="citations" />
118 </tool> 137 </tool>