diff gen_headers_after_merge_priors_one_comparate.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/gen_headers_after_merge_priors_one_comparate.xml	Thu Jan 14 21:51:36 2021 +0000
@@ -0,0 +1,115 @@
+<tool id="base_gen_headers_one_comparate" name="Generate Headers" version="21.1.13">
+    <description>for one condition to test for Allelic Imbalance</description>
+    <macros>
+      <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command><![CDATA[
+    mkdir outputs;
+    cd outputs;
+    gen_headers_after_merge_priors_one_comparate.py
+    --output=`pwd`
+    --collection_identifiers="${','.join($collection.keys())}"
+    --collection_filenames="${",".join(map(str, $collection))}"
+    --design=$design
+]]></command>
+    <inputs>
+        <param name="collection" type="data_collection" collection_type="list" label="Collection from Merge Prior to Comparate" help="Select the collection of files with the ASE Count Tables merged to Prior Calculations for the comparate [Required]"/>
+        <param name="design" type="data" format="tabular,tsv" label="Comparate Design file" help="Enter the Comparate Design file for one condition; formatting is below [Required]"/>
+    </inputs>
+    <outputs>
+      <collection name="split_output" type="list" label="${tool.name} on ${on_string}: Generate Headers for One Comparate">
+        <discover_datasets pattern="(?P&lt;name&gt;bayesian_input_.*)" ext="tabular" directory="outputs" />
+      </collection>
+    </outputs>
+    <tests>
+        <test>
+            <param name="design" value="bayesian_input/comparate_df_one_condition.tsv" ftype="tsv"/>
+            <param name="collection" value="merge_priors_testdata/bayesian_input_W55_M" ftype="tabular"/>
+            <output_collection name="split_output" type="list">
+              <element name="FEATURE_ID">
+                <assert_contents>
+                  <has_text_matching expression="gen_headers_one_comparate"/>
+                </assert_contents>
+              </element>
+             </output_collection>
+        </test>
+    </tests>
+    <help><![CDATA[
+**Tool Description**
+
+The *Generate Headers for ONE Comparate* tool takes an output file created for a single user-specified comparate in the *Merge Priors to Comparate tool* and creates the
+headers needed for the running the Bayesian model.
+
+**NOTE:** This tool is only for user's wishing to test allelic imbalance for only one condition (ie W55_M). If testing for two or more conditions use the
+*Merge Two or More Comparate Datasets and Generate Headers* tool.
+
+    **Required Inputs**
+
+**Collection of Merged Prior to Comparate Files [REQUIRED]**
+
+The output from the *Merge Prior to Comparate* tool is required.
+
+Example of a file containing priors merged to comparate data (W55_Mated)::
+
+	FEATURE_ID	prior_W55_M_both	prior_W55_M_g1             prior_W55_M_g2	W55_M_flag_analyze     W55_M_num_reps   	W55_M_g1_total_rep1     	W55_M_g2_total_rep1     	W55_M_both_total_rep1       	W55_M_flag_apn_rep1     	W55_M_APN_total_reads_rep1	W55_M_APN_both_rep1	W55_M_g1_total_rep2     	W55_M_g2_total_rep2     	W55_M_both_total_rep2   	W55_M_flag_apn_rep2     	W55_M_APN_total_reads_rep2     	W55_M_APN_both_rep2
+	l(1)G0196	0.802196053469128	0.114417568427753         0.0833863781031191	1    	        	2			691				519				5020 	        		1   				29.073464805232			23.4243873865079		1075				812				7481				1			43.7266913990042		34.9168212437762
+	CG8920  	0.866028708133971	0.0344497607655502        0.0995215311004785	1			2			29				 62				 647    			1				10.3878993081113		9.10716914470779		38				126				920				1			15.2470189901369		12.9534815250994
+	CG10932 	0.821591948764867	0.108417200365965         0.0699908508691674	1			2			163				122		                1112		    		1				89.9299663299663		71.5858585858586		237				134				1881				1 			144.974410774411		121.086195286195
+
+
+
+**Comparate Design File [REQUIRED]**
+
+This tool requires a Comparate design file created by the user that contains the desired comparates. The comparates are the genomes that the user wishes to be
+tested as a condition to be compared  in Bayesian model for allelic specific expression.
+
+**NOTE**: The Comparate Design File must be created and supplied by the user. It must explicitly list the comparate condition that the user wants to compare.
+
+    The design file must contain the following columns, in order::
+
+    (1) Comparate_1: comparate 1 identifier (ex. W55_M)
+    (2) CompID: An unique identifier that specifies the comparison (ex. W55_M)
+
+*CompID* is the same as the comparate_1 when testing allelic specific expression for only one condition
+
+
+An example design file:
+
+    +-------------+--------+
+    | Comparate_1 | compID |
+    +=============+========+
+    | W55_M       | W55_M  |
+    +-------------+--------+
+    | W55_V       | W55_V  |
+    +-------------+--------+
+
+**OUTPUTS**
+
+This tool outputs one file:
+
+(1) A TSV file with the Merged Priors to Comparate output with new headers needed for Bayesian Model tool.
+
+Example of output::
+
+
+    +-------------+-----------------+-------------------+--------------------+-----------------+-------------+------------------+-------------------+--------------------+------------------+-------------------------+---------------------+------------------+-------------------+--------------------+-------------------+--------------------------+------------------+
+    | Feature_ID  | prior_c1_both   | prior_c1_g1       | prior_c1_g2        | c1_flag_analyze | c1_num_reps | c1_g1_total_rep1 | c1_g2_total_rep1  | c1_both_total_rep1 | c1_flag_apn_rep1 | c1_APN_total_reads_rep1 | c1_APN_both_rep1    | c1_g1_total_rep2 | c1_g2_total_rep2  | c1_both_total_rep2 | c1_flag_apn_rep2  | c1_APN_total_reads_rep2  | c1_APN_both_rep2 |
+    +-------------+-----------------+-------------------+--------------------+-----------------+-------------+------------------+-------------------+--------------------+------------------+-------------------------+---------------------+------------------+-------------------+--------------------+-------------------+--------------------------+------------------+
+    |l(1)G1096    |0.799907266902715| 0.118361153262519 | 0.0817315798347665 |        1        |       2     |        295       |         234       |        2197        |         1        |     12.7234208727912    | 10.2551010446158    |        1885      |        1165       |        12201       |         1         | 71.2019427901982         | 56.9617787757493 |
+    +-------------+-----------------+-------------------+--------------------+-----------------+-------------+------------------+-------------------+--------------------+------------------+-------------------------+---------------------+------------------+-------------------+--------------------+-------------------+--------------------------+------------------+
+    | CG10932     |0.853881278538813| 0.0597412480974125| 0.0863774733637747 |        1        |       2     |         13       |          39       |         308        |         1        |     5.06815839835124    | 4.33534520830266    |         100      |         134       |         1394       |         1         | 22.9213896658325         | 19.6266745178861 |
+    +-------------+-----------------+-------------------+--------------------+-----------------+-------------+------------------+-------------------+--------------------+------------------+-------------------------+---------------------+------------------+-------------------+--------------------+-------------------+--------------------------+------------------+
+    | CG8920      |0.808955223880597| 0.123383084577114 | 0.0676616915422886 |        1        |       2     |         93       |          20       |         500        |         1        |     39.4720538720539    | 32.1912457912458    |         347      |         257       |         2633       |         1         | 208.422222222222         | 169.53063973064  |
+    +-------------+-----------------+-------------------+--------------------+-----------------+-------------+------------------+-------------------+--------------------+------------------+-------------------------+---------------------+------------------+-------------------+--------------------+-------------------+--------------------------+------------------+
+
+    ]]></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>