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Commit message:
Deleted selected files |
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removed:
SAINT_preprocessing_v5.xml |
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| diff -r 13383ba55336 -r a1bcd44fc605 SAINT_preprocessing_v5.xml --- a/SAINT_preprocessing_v5.xml Tue Nov 17 10:32:56 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,91 +0,0 @@ -<tool id="SAINT_preprocessing_v5" name="SAINT pre-processing"> - <description></description> - <command interpreter="python"> - #if (str($type) == 'Scaffold'): - SAINT_preprocessing_v6.py $input $preybool $fasta_db $Inter_file $Prey_file - " - #for $ba in $bait - ${ba.bait1} - ${ba.assign} - ${ba.T_C} - #end for - " - $Bait_file \$INSTALL_RUN_PATH/ - #elif (str($type) == 'MaxQuant'): - SAINT_preprocessing_v6_mq_pep.py $input $preybool $fasta_db $Inter_file $Prey_file - " - #for $ba in $bait - ${ba.bait1} - ${ba.assign} - ${ba.T_C} - #end for - " - $Bait_file \$INSTALL_RUN_PATH/ - #end if - </command> - <requirements> - <requirement type="set_environment">INSTALL_RUN_PATH</requirement> - </requirements> - <inputs> - <param type="select" name="type" label="MaxQuant or Scaffold"> - <option value="MaxQuant">MaxQuant</option> - <option value="Scaffold">Scaffold</option> - </param> - <param format="dat" name="input" type="data" label="Scaffold or MaxQuant proteinGroup Output"/> - <param type="boolean" name="preybool" checked="true" label="Create Prey File"/> - <param type="data" name="fasta_db" format="fasta" label="Provide Uniprot Fasta database" /> - <repeat name="bait" title="Bait Create"> - <param name="bait1" type="text" size="100"/> - <param name="assign" type="text" size="100"/> - <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"/> - <data format="txt" name="Prey_file" label="Prey File" /> - <data format="txt" name="Bait_file" label="Bait File" /> - </outputs> - <stdio> - <regex match="error" - source="stdout" - level="fatal" - description="Unknown error"/> - <regex match="Error: bad bait" - source="stdout" - level="fatal" - description="Error: bad bait"/> - </stdio> - - <tests> - <test> - <param name="input" value="fa_gc_content_input.fa"/> - <output name="out_file1" file="fa_gc_content_output.txt"/> - </test> - </tests> - <help> -Pre-processing: -APOSTL is able to recognize either a Scaffold "Samples Report" file (tab-delimited -txt file) or the "peptides.txt" file output in the maxquant "txt" output folder. No -modifications should be made to these files. Using the "Bait Create" tool, you can -create your "bait.txt" file. It is important that the individual bait names match the -bait names within your scaffold or maxquant output. APOSTL uses the bait file to find -the user's baits of interest. Additionally there is an option to make the prey file (Y/N). -When making a prey file, APOSTL queries uniprot in order to extract protein amino acid -lengths and gene names. This takes several minutes depending on your internet connection. -Some users may want to run SAINTexpress using the same data set while changing which baits -are considered test or control. It is useful to toggle "Make Prey" off in order to save -time by circumventing this step as the same prey file can be used for both SAINTexpress -runs. - -INPUTS: - -Scaffold file: - -- Scaffold "Samples Report" output (tab-delimited txt file) - - -Maxquant file: - -- maxquant "peptides.txt" file (tab-delimited txt file) - </help> -</tool> |