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SAINT_preprocessing_v5.xml |
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| diff -r 378db8ea92ea -r 2b631809150b SAINT_preprocessing_v5.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SAINT_preprocessing_v5.xml Tue Nov 10 13:14:22 2015 -0500 |
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| @@ -0,0 +1,91 @@ +<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</requirment> + </requirments> + <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> |