|
0
|
1 <tool id="scaffold_export" name="Scaffold Export" version="0.1.0">
|
|
|
2 <description>
|
|
|
3 Export summary from Scaffold SF3 file.
|
|
|
4 </description>
|
|
|
5 <macros>
|
|
|
6 <import>macros.xml</import>
|
|
|
7 </macros>
|
|
|
8 <command interpreter="python">
|
|
|
9 scaffold_wrapper.py export \
|
|
|
10 --sf3 $sf3_input \
|
|
|
11 --output $output \
|
|
|
12 --export_type $export.export_type \
|
|
|
13 ## Begin Threshold Parameters
|
|
|
14 #set $threshold_type = $threshold.type
|
|
|
15 #set $threshold_options = $threshold
|
|
|
16 #if $threshold_type != "none"
|
|
|
17 --protein_probability=$threshold_options.protein_probability \
|
|
|
18 --peptide_probability=$threshold_options.peptide_probability \
|
|
|
19 --minimum_peptide_count=$threshold_options.minimum_peptide_count \
|
|
|
20 #if $threshold_type != "simple"
|
|
|
21 $threshold_options.ignore_charge_1 \
|
|
|
22 $threshold_options.ignore_charge_2 \
|
|
|
23 $threshold_options.ignore_charge_3 \
|
|
|
24 $threshold_options.ignore_charge_4 \
|
|
|
25 --minimum_ntt=$threshold_options.minimum_ntt \
|
|
|
26 --minimum_peptide_length=$threshold_options.minimum_peptide_length \
|
|
|
27 #end if
|
|
|
28 #end if
|
|
|
29 ## End Threshold Parameters
|
|
|
30 </command>
|
|
|
31 <inputs>
|
|
|
32 <param format="sf3" name="sf3_input" type="data" label="Scaffold Results" />
|
|
|
33 <conditional name="export">
|
|
|
34 <param name="export_type" type="select" label="Export Format">
|
|
|
35 <option value="mzIdentML">MzIdentML</option>
|
|
|
36 <option value="protxml">ProtXML</option>
|
|
|
37 <option value="statistics">Stastics (tabular)</option>
|
|
|
38 <option value="spectrum-report">Spectrum Report (tabular)</option>
|
|
|
39 <option value="peptide-report">Peptide Report (tabular)</option>
|
|
|
40 <option value="protein-report">Protein Report (tabular)</option>
|
|
|
41 <option value="publication-report">Publication Report (tabular)</option>
|
|
|
42 <option value="isoform-report">Isoform Report (tabular)</option>
|
|
|
43 <option value="spectrum-counting-report">Spectrum Counting Report (tabular)</option>
|
|
|
44 <option value="accession-report">Accession Report (tabular)</option>
|
|
|
45 <option value="experiment-report">Experiment Report (tabular)</option>
|
|
|
46 </param>
|
|
|
47 </conditional>
|
|
|
48 <expand macro="threshold" />
|
|
|
49 </inputs>
|
|
|
50 <outputs>
|
|
|
51 <data format="tabular" name="output">
|
|
|
52 <change_format>
|
|
|
53 <when input="export.export_type" value="mzIdentML" format="mzid" />
|
|
|
54 <when input="export.export_type" value="protxml" format="protxml" />
|
|
|
55 </change_format>
|
|
|
56 </data>
|
|
|
57 </outputs>
|
|
|
58 <requirements>
|
|
|
59 <requirement type="package">scaffold</requirement>
|
|
|
60 </requirements>
|
|
|
61 <help>
|
|
|
62 **What it does**
|
|
|
63
|
|
|
64 Export data out of Scaffold's binary data format (sf3) into tabular reports or XML.
|
|
|
65
|
|
|
66 ------
|
|
|
67
|
|
|
68
|
|
|
69 **Citation**
|
|
|
70
|
|
|
71 For the underlying tool, please cite `TODO`
|
|
|
72
|
|
1
|
73 If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/scaffold
|
|
0
|
74 </help>
|
|
1
|
75 </tool>
|
