| Previous changeset 7:aa9875d90894 (2016-09-19) Next changeset 9:ce0a125b3cd1 (2016-09-19) |
|
Commit message:
Uploaded |
|
added:
FC_Filter_IsoDE_wrapper.xml |
| b |
| diff -r aa9875d90894 -r dc8efad9c31b FC_Filter_IsoDE_wrapper.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/FC_Filter_IsoDE_wrapper.xml Mon Sep 19 22:09:41 2016 -0400 |
| b |
| @@ -0,0 +1,56 @@ +<tool id="FC_Filter_IsoDE2" name="Fold Change Filter"> + <description>Filters IsoDE2 output based on fold change</description> + <command interpreter="bash"> + FC_Filter_IsoDE_wrapper.sh $input1 $input2 $out_file $FC_min + </command> + <inputs> + + <param name="input1" type="data" label="Select data from IsoDE output files" /> + <param name="input2" type="select" label="A list of genes/isoforms over expressed in:"> + <option value="1">Condition 1</option> + <option value="2">Condition 2</option> + <option value="3">Condition 1 or Condition 2</option> + </param> + <param name="FC_min" type="integer" value="2" label="Minimum Fold change:" /> + </inputs> + + <outputs> + <data format="tabular" name="out_file" metadata_source="input1" label="Filtered IsoDE" /> + </outputs> + + +<help> +**What it does** + +This filter selects from the IsoDE2 output file, genes that genes that have fold change (ratio between the gene expression in the two conditions in comparison) greater +than or equal to the a certain threshold set by the user. + + +**Input** + +* 1- IsoDE2 output file. It can be any of the output files generated by an IsoDE2 runs; for genes or isoforms/FPKM or TPM +* 2- Direction of over expression of interest to the user (genes over expressed in condition1, over expressed in condition 2, or overexpressed in either condition) +* 3- Minimim fold change of interest +* +* + + + + +**Output** + + +The output is a tabular file with the same fields as the input file, containing the subset of genes satisfying the conditions specified by the used. + +</help> +</tool> + + + + + + + + + + |