| Previous changeset 60:3c0ed536029e (2016-08-27) Next changeset 62:81db20bfc349 (2016-08-27) |
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Commit message:
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modified:
SAINT_preprocessing.xml |
| b |
| diff -r 3c0ed536029e -r 0b4450bdc6a9 SAINT_preprocessing.xml --- a/SAINT_preprocessing.xml Sat Aug 27 21:29:26 2016 -0400 +++ b/SAINT_preprocessing.xml Sat Aug 27 21:38:03 2016 -0400 |
| b |
| @@ -2,7 +2,7 @@ <description></description> <command interpreter="python"> #if (str($type_select.type) == 'Scaffold'): - SAINT_preprocessing.py $input $preybool $fasta_db $Inter_file $Prey_file + SAINT_preprocessing.py $type_select.input $type_select.preybool $type_select.fasta_db $type_select.Inter_file $type_select.Prey_file " #for $ba in $bait ${ba.bait1} @@ -10,9 +10,9 @@ ${ba.T_C} #end for " - $Bait_file \$INSTALL_RUN_PATH/ $bait_bool $bait_file_in + $type_select.Bait_file \$INSTALL_RUN_PATH/ $type_select.bait_bool $type_select.bait_file_in #elif (str($type_select.type) == 'MaxQuant'): - SAINT_preprocessing_mq_pep.py $input $preybool $fasta_db $Inter_file $Prey_file + SAINT_preprocessing_mq_pep.py $type_select.input $type_select.preybool $type_select.fasta_db $type_select.Inter_file $type_select.Prey_file " #for $ba in $bait ${ba.bait1} @@ -20,9 +20,9 @@ ${ba.T_C} #end for " - $Bait_file \$INSTALL_RUN_PATH/ $bait_bool $bait_file_in + $type_select.Bait_file \$INSTALL_RUN_PATH/ $type_select.bait_bool $type_select.bait_file_in #elif (str($type_select.type) == 'Peptideshaker'): - Protein_report_processing.py "$input" $Bait_file $use_metric $fasta_db $preybool + Protein_report_processing.py "$type_select.input" $type_select.Bait_file $type_select.use_metric $type_select.fasta_db $type_select.preybool " #for $ba in $bait ${ba.bait1} @@ -30,7 +30,7 @@ ${ba.T_C} #end for " - \$INSTALL_RUN_PATH/ $bait_bool $bait_file_in $Inter_file $Prey_file + \$INSTALL_RUN_PATH/ $type_select.bait_bool $type_select.bait_file_in $type_select.Inter_file $type_select.Prey_file #end if </command> <requirements> @@ -49,11 +49,6 @@ <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"/> - <repeat name="bait" title="Bait Create"> - <param name="bait1" type="text" size="100" label="Bait"/> - <param name="assign" type="text" size="100" label="Group Assignment"/> - <param name="T_C" type="boolean" checked="true" label="Is this a Control?"/> - </repeat> </when> <when value="Scaffold"> <param format="dat" name="input" type="data" label="Scaffold Output"/> @@ -61,11 +56,6 @@ <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"/> - <repeat name="bait" title="Bait Create"> - <param name="bait1" type="text" size="100" label="Bait"/> - <param name="assign" type="text" size="100" label="Group Assignment"/> - <param name="T_C" type="boolean" checked="true" label="Is this a Control?"/> - </repeat> </when> <when value="Peptideshaker"> <param format="dat" name="input" type="data" label="Peptideshaker Output" multiple="true"/> @@ -80,13 +70,13 @@ <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"/> - <repeat name="bait" title="Bait Create"> - <param name="bait1" type="text" size="100" label="Bait"/> - <param name="assign" type="text" size="100" label="Group Assignment"/> - <param name="T_C" type="boolean" checked="true" label="Is this a Control?"/> - </repeat> </when> </conditional> + <repeat name="bait" title="Bait Create"> + <param name="bait1" type="text" size="100" label="Bait"/> + <param name="assign" type="text" size="100" label="Group Assignment"/> + <param name="T_C" type="boolean" checked="true" label="Is this a Control?"/> + </repeat> </inputs> <outputs> <data format="txt" name="Inter_file" label="Inter File"/> |