| Previous changeset 0:da1c63d00c1b (2016-08-11) Next changeset 2:8bf642eee8eb (2016-08-11) |
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consol_fit.xml |
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| diff -r da1c63d00c1b -r c5d9dd4b6a5a consol_fit.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/consol_fit.xml Thu Aug 11 18:07:39 2016 -0400 |
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| @@ -0,0 +1,81 @@ +<tool id="consolidate_fitnesses" name="Consolidate Fitnesses"> + <description>of transposon insertion locations</description> + <requirements> + <requirement type="package" version="1.64">biopython</requirement> + </requirements> + <command interpreter="python"> + consol_fit.py + -i $input + -calctxt $calctxt + -out $output + -out2 $output2 + -maxweight $maxweight + -cutoff $cutoff + -cutoff2 $cutoff2 + -wig $output3 + #if $normalization.calculations == "yes": + -normalize $normalization.genes + #end if + #if $multiply.choice == "yes": + -multiply $multiply.factor + #end if + #if $reads.downstream == "yes": + -d 1 + #end if + </command> + <inputs> + <param name="input" type="data" label="Fitness file"/> + <param name="calctxt" type="data" label="the txt file output from calc_fitness"/> + <conditional name="normalization"> + <param name="calculations" type="select" label="Normalize fitness calculations?"> + <option value="no">No</option> + <option value="yes">Yes</option> + </param> + <when value="no"> + <!-- do nothing --> + </when> + <when value="yes"> + <param name="genes" type="data" label="Genes to normalize by" /> + </when> + </conditional> + <param name="cutoff" type="float" value="0.0" label="Cutoff"/> + <param name="cutoff2" type="float" value="0.0" label="Cutoff2"/> + <param name="maxweight" type="float" value="75" label="Maximum weight of a transposon gene in normalization calculations"/> + <conditional name="multiply"> + <param name="choice" type="select" label="Multiply fitness scores by a certain value?"> + <option value="no">No</option> + <option value="yes">Yes</option> + </param> + <when value="no"> + <!-- do nothing --> + </when> + <when value="yes"> + <param name="factor" type="float" value="0.0" label="Multiply by" /> + </when> + </conditional> + <conditional name="reads"> + <param name="downstream" type="select" label="Are all reads downstream of the transposon?"> + <option value="no">No</option> + <option value="yes">Yes</option> + </param> + <when value="no"> + <!-- do nothing --> + </when> + <when value="yes"> + <!-- do nothing --> + </when> + </conditional> + </inputs> + <outputs> + <data format="csv" name="output" /> + <data format="txt" name="output2" /> + <data format="wig" name="output3" /> + </outputs> + <help> + +**What it does** + +This tool consolidates the fitness values of transposon insertion mutations generated by Tn-Seq, and is mostly useful for consolidating values produced by a 4-cycle looping trimming pipeline. + +</help> +</tool> \ No newline at end of file |