Mercurial > repos > galaxyp > scaffold
comparison scaffold_export.xml @ 0:e9981e6af666 draft
Improved some datatype handling
| author | galaxyp |
|---|---|
| date | Thu, 20 Jun 2013 11:07:47 -0400 |
| parents | |
| children | 0d0cbb69a03f |
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| -1:000000000000 | 0:e9981e6af666 |
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| 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 | |
| 73 If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-scaffold | |
| 74 </help> | |
| 75 </tool> |