| Previous changeset 78:211fd8ae6edc (2017-03-02) Next changeset 80:6ad498eac0e2 (2017-05-06) |
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modified:
SAINT_preprocessing.xml |
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| diff -r 211fd8ae6edc -r a51c0e6d7d99 SAINT_preprocessing.xml --- a/SAINT_preprocessing.xml Thu Mar 02 16:03:07 2017 -0500 +++ b/SAINT_preprocessing.xml Fri May 05 20:13:24 2017 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="SAINT_preprocessing_v5" name="SAINT pre-processing"> +<tool id="SAINT_preprocessing_v6" name="SAINT pre-processing"> <description></description> <command interpreter="python"> #if (str($type_select.type) == 'Scaffold'): @@ -31,6 +31,22 @@ #end for " \$INSTALL_RUN_PATH/ $type_select.bait_bool $type_select.bait_file_in $Inter_file $Prey_file + #elif (str($type_select.type) == 'Peptideshaker_ordered_input'): + Protein_report_processing.py + #set $protein_files=[] + #for $i1, $protein_input in enumerate($type_select.protein_inputs) + #silent $protein_files.append(str($protein_input.protein_file)) + #end for + #echo ','.join($protein_files) + $Bait_file $type_select.use_metric $type_select.fasta_db $type_select.preybool + " + #for $ba in $bait + ${ba.bait1} + ${ba.assign} + ${ba.T_C} + #end for + " + \$INSTALL_RUN_PATH/ $type_select.bait_bool $type_select.bait_file_in $Inter_file $Prey_file #elif (str($type_select.type) == 'mzIdentML'): mzID_process2.py "$type_select.input" $type_select.bait_file_in $type_select.preybool $type_select.fasta_db \$INSTALL_RUN_PATH/ " @@ -82,6 +98,22 @@ <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="Peptideshaker_ordered_input"> + <repeat name = "protein_inputs" min="1" title="Input PeptideShaker Protein Result File"> + <param format="tabular" name="protein_file" type="data" label="Peptideshaker Output" multiple="false"/> + </repeat> + <param type="select" name="use_metric" label="Select Report File Value for Quantification"> + <option value="Validated_Peptides">#Validated Peptides</option> + <option value="Peptides">#Peptides</option> + <option value="Unique">#Unique</option> + <option value="Validated_PSMs">#Validated PSMs</option> + <option value="PSMs">#PSMs</option> + </param> + <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> <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"/> |