Mercurial > repos > bornea > saint_preprocessing
changeset 63:1972ccdbeb16 draft
Uploaded
| author | bornea |
|---|---|
| date | Sat, 27 Aug 2016 22:12:01 -0400 |
| parents | 81db20bfc349 |
| children | e382e24af909 |
| files | SAINT_preprocessing.xml |
| diffstat | 1 files changed, 18 insertions(+), 0 deletions(-) [+] |
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--- a/SAINT_preprocessing.xml Sat Aug 27 21:42:13 2016 -0400 +++ b/SAINT_preprocessing.xml Sat Aug 27 22:12:01 2016 -0400 @@ -31,6 +31,16 @@ #end for " \$INSTALL_RUN_PATH/ $type_select.bait_bool $type_select.bait_file_in $Inter_file $Prey_file + #elif (str($type_select.type) == 'mzIdentML'): + Protein_report_processing.py "$type_select.input" $type_select.bait_file_in $type_select.preybool $type_select.fasta_db \$INSTALL_RUN_PATH/ + " + #for $ba in $bait + ${ba.bait1} + ${ba.assign} + ${ba.T_C} + #end for + " + $type_select.bait_bool $Prey_file $Bait_file $Inter_file #end if </command> <requirements> @@ -42,6 +52,7 @@ <option value="MaxQuant">MaxQuant</option> <option value="Scaffold">Scaffold</option> <option value="Peptideshaker">Peptideshaker</option> + <option value="mzIdentML">mzIdentML</option> </param> <when value="MaxQuant"> <param format="dat" name="input" type="data" label="MaxQuant peptides Output"/> @@ -71,6 +82,13 @@ <param name="bait_bool" type="boolean" checked="true" label="Are You Providing Your Own bait file?"/> <param type="data" format="dat" name="bait_file_in" label="Bait File" optional="true"/> </when> + <when value="mzIdentML"> + <param format="dat" name="input" type="data" label="mzIdentML Files" multiple="true"/> + <param type="boolean" name="preybool" checked="true" label="Create Prey File"/> + <param type="data" name="fasta_db" format="fasta" label="Provide Uniprot Fasta database" optional="true"/> + <param name="bait_bool" type="boolean" checked="true" label="Are You Providing Your Own bait file?"/> + <param type="data" format="dat" name="bait_file_in" label="Bait File" optional="true"/> + </when> </conditional> <repeat name="bait" title="Bait Create"> <param name="bait1" type="text" size="100" label="Bait"/>