diff check_comparate_design_file.xml @ 0:e979cb57a5d5 draft default tip

"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/check_comparate_design_file.xml	Thu Jan 14 21:51:36 2021 +0000
@@ -0,0 +1,65 @@
+<tool id="base_check_comparate_design_file" name="Check Comparate Design File" version="21.1.13">
+    <description>for correct formatting and header names </description>
+    <macros>
+      <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command><![CDATA[
+    check_comparate_design_file.py
+    --design=$design
+    --compNum=$compNum
+    --out=$out
+]]></command>
+    <inputs>
+        <param name="design" type="data" format="tabular,tsv" label="Select Comparate Design File" help="Design file containing comparates and conditions. Please refer to the BASE User Guide for help."/>
+        <param name="compNum" size="30" type="select" value="" display="radio" label="Comparate Number" help="Select the number of comparate conditions for the data.">
+            <option value="1">One Comparate</option>
+            <option value="2">Two Comparates</option>
+        </param>
+    </inputs>
+    <outputs>
+        <data format="tabular" name="out" label="${tool.name} on ${on_string}: Comparate Design criteria"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="design" ftype="data" value="check_comparate_design_file/df_comparate.tsv"/>
+            <param name="compNum" ftype="text" value="1"/>
+            <output name="out" />
+        </test>
+    </tests>
+    <help><![CDATA[
+**Tool Description**
+
+This tool checks to make sure the design file is formatted correctly and has all needed headers. It also verifies that there are no missing labels.
+
+**The design file should contain the following columns, in order:**
+
+
+    (5) Comparate_1: first comparate. For example, 'W55_M' which is a combination of genotype W55 and condition mated.
+    (6) Comparate_2: second comparate.  For example 'W55_V' which is a combination of genotype W55 and condition virgin
+    (7) CompID: A unique identifier that describes the comparison. For example, 'W55_M_V', for the comparison of W55 mated to W55 virgin.
+
+
+
+An example design file for two comparates::
+
+	Comparate_1   Comparate_2	 compID
+	W55_M	      W55_V	         W55_M_V
+
+
+**Outputs**
+
+	(1) a logfile with information about whether the column names are correct
+	(2) a text file containing a list of any missing or misspelled labels, if present
+
+    ]]></help>
+    <citations>
+            <citation type="bibtex">@ARTICLE{Miller20BASE,
+            author = {Brecca Miller, Alison M. Morse, Elyse Borgert, Zihao Liu, Kelsey Sinclair, Gavin Gamble, Fei Zou, Jeremy Newman, Luis Leon Novello, Fabio Marroni, Lauren M. McIntyre},
+            title = {Testcrosses are an efficient strategy for identifying cis regulatory variation: Bayesian analysis of allele imbalance among conditions (BASE)},
+            journal = {????},
+            year = {submitted for publication}
+            }
+            </citation>
+    </citations>
+</tool>