diff ttest_perm.xml @ 1:2e7d47c0b027 draft

"planemo upload for repository https://[e-mail]/repos/malex/secimtools"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ttest_perm.xml	Mon Mar 08 22:04:06 2021 +0000
@@ -0,0 +1,92 @@
+<tool id="secimtools_ttest_perm" name="Group Comparison by Permutation" version="@WRAPPER_VERSION@">
+    <description>on features.</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+ttest_perm.py
+--input $input
+--design $design
+--uniqueID $uniqueID
+--group $group
+--reps $reps
+--summaries $summaries
+--flags $flags
+--volcano $volcano
+    </command>
+    <inputs>
+        <param name="input" type="data" format="tabular" label="Wide Dataset" help="Input dataset in wide format and tab separated. If file is not tab separated see TIP below."/>
+        <param name="design" type="data" format="tabular" label="Design File" help="Design file tab separated. Note you need a 'sampleID' column. If not tab separated see TIP below."/>
+        <param name="uniqueID" type="text" size="30" value="" label="Unique Feature ID"  help="Name of the column in your Wide Dataset that has unique Feature IDs."/>
+        <param name="group" type="text" size="30"             label="Group/Treatment"    help="Name of the column in your Design File that contains group classifications."/>
+        <param name="reps"  type="text" size="30"    value="" label ="Iteration Number." help="Enter the number of iterations you want to carry out."/>
+    </inputs>
+    <outputs>
+        <data format="tabular" name="summaries" label="${tool.name} on ${on_string}: Summaries that include p-values and mean differences."/>
+        <data format="tabular" name="flags" label="${tool.name} on ${on_string}: Flags that include 0.01,  0.05 and  0.10 significance levels for the differences. "/>
+        <data format="pdf" name="volcano" label="${tool.name} on ${on_string}: Volcano plots for the differences."/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input"    value="fly_test_sbys.tsv"/>
+            <param name="design"   value="fly_test_design.tsv"/>
+            <param name="uniqueID" value="rowID" />
+            <param name="group"    value="mating_source" />
+            <param name="reps"     value="1000" />
+            <output name="summaries" file="fly_ttest_permuted_summary.tsv" />
+            <output name="flags"     file="fly_ttest_permuted_flags.tsv" />
+            <output name="volcano"   file="fly_ttest_permuted_volcano.pdf" compare="sim_size" delta="10000"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+@TIP_AND_WARNING@
+
+**Tool Description**
+
+The tool performs a permuted two-sided t-test for multiple (two or more) groups of independent sample (unpaired or independent t-test).
+The user selects the number of iterations to perform.
+
+In an unpaired t-test the samples within and between groups are independent.  The p-value is calculated by permutation of the data.
+The permutation test is performed for all pairs of conditions specified using the Group/Treatment field and for the number of specified iterations.
+If there are three treatment conditions (Control, Time1 and Time2) then t-tests will be performed for: (i) Control vs Time1, (ii) Control vs Time2, and (iii) Time1 vs Time2.
+Note that this will give slightly different results than the contrast in an ANOVA because the ANOVA uses all groups to estimate the error.
+
+--------------------------------------------------------------------------------
+
+**Input**
+
+    - Two input datasets are required.
+
+
+@WIDE@
+
+**NOTE:** The sample IDs must match the sample IDs in the Design File
+(below). Extra columns will automatically be ignored.
+
+@METADATA@
+
+@UNIQID@
+
+**Group/Treatment**
+
+        - List with the name of the column the Design File that contains group classifications.
+
+** Reps**
+ 
+        - Number of iterations (permutations) to carry out
+
+--------------------------------------------------------------------------------
+
+**Output**
+
+The tool outputs 3 files:
+
+(1) a TSV file with the results table containing p-values for each test and the corresponding differences between the means for comparisons between the groups.
+(2) a TSV file with an indicator flag = 1 if the difference between the groups is statistically significant using provided α levels.
+(3) a PDF file with volcano plots visual inspection of the differences between group means and p-values. The red dashed line in volcano plot(s) corresponds to a p-value = 0.01 cutoff (2 on the negative log base 10 scale).
+
+    ]]></help>
+    <expand macro="citations"/>
+</tool>