Mercurial > repos > proteore > proteore_ms_observation_pepatlas
comparison Get_ms-ms_observations.xml @ 5:034cfb96a482 draft
planemo upload commit b052261cf5cd6c2413e301a19d5c95d9794f1e81-dirty
author | proteore |
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date | Wed, 13 Mar 2019 09:34:37 -0400 |
parents | 299eb4a62e0c |
children | e77c0f3e9bab |
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4:299eb4a62e0c | 5:034cfb96a482 |
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1 <tool id="retr_pepatlas1" name="Get MS/MS observations in tissue/fluid" version="2019.02.01.1"> | 1 <tool id="retr_pepatlas1" name="Get MS/MS observations in tissue/fluid" version="2019.02.26"> |
2 <description>[Peptide Atlas]</description> | 2 <description>[Peptide Atlas]</description> |
3 <requirements> | 3 <requirements> |
4 <requirement type="package" version="3.4.1">R</requirement> | 4 <requirement type="package" version="3.4.1">R</requirement> |
5 </requirements> | 5 </requirements> |
6 <stdio> | 6 <stdio> |
14 #else | 14 #else |
15 --input="$input.file" | 15 --input="$input.file" |
16 --column_number="$input.ncol" | 16 --column_number="$input.ncol" |
17 --header="$input.header" | 17 --header="$input.header" |
18 #end if | 18 #end if |
19 --atlas=${",".join([$__tool_directory__+"/"+str(ref) for ref in str($atlas).split(",")])} | 19 --atlas=${",".join([str(ref) if "peptide_atlas" in str(ref).split("/") else $__tool_directory__+"/"+str(ref) for ref in str($atlas).split(",")])} |
20 --output="$output" | 20 --output="$output" |
21 </command> | 21 </command> |
22 | 22 |
23 <inputs> | 23 <inputs> |
24 <conditional name="input" > | 24 <conditional name="input" > |
39 </param> | 39 </param> |
40 </when> | 40 </when> |
41 <when value="file" > | 41 <when value="file" > |
42 <param name="file" type="data" format="txt,tabular" label="Select your file" help="" /> | 42 <param name="file" type="data" format="txt,tabular" label="Select your file" help="" /> |
43 <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does file contain header?" /> | 43 <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does file contain header?" /> |
44 <param name="ncol" type="text" value="c1" label="Column of IDs" help='For example, fill in "c1" if it is the first column, "c2" if it is the second column and so on' /> | 44 <param name="ncol" type="text" value="c1" label="Column of IDs" help='For example, fill in "c1" if it is the first column, "c2" if it is the second column and so on'> |
45 <validator type="regex" message="Please enter a column number, for example: 'c1' for the first column">[c]{0,1}[0-9]+</validator> | |
46 </param> | |
45 </when> | 47 </when> |
46 </conditional> | 48 </conditional> |
47 <!-- Peptide Atlas options --> | 49 <!-- Peptide Atlas options --> |
48 <param name="atlas" type="select" display="checkboxes" multiple="true" label="Proteomics dataset (biological sample)" optional="false" > | 50 <param name="atlas" type="select" display="checkboxes" multiple="true" label="Proteomics dataset (biological sample)" optional="false" > |
49 <options from_data_table="proteore_peptide_atlas"> | 51 <options from_data_table="proteore_peptide_atlas"> |