diff merge_comparates_and_gen_headers_for_bayesian.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/merge_comparates_and_gen_headers_for_bayesian.xml	Thu Jan 14 21:51:36 2021 +0000
@@ -0,0 +1,109 @@
+<tool id="merge_comparates_and_gen_headers_for_bayesian" name="Merge Comparate Datasets and Generate Headers" version="21.1.13">
+    <description>for Bayesian Analysis of Allelic Imbalance</description>
+    <macros>
+      <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command><![CDATA[
+    mkdir outputs;
+    cd outputs;
+    merge_comparates_generate_bayesian_headers.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 of Comparate Datasets containing Prior Probability Estimates" help="Select the collection containing files to be merged. [Required]"/>
+        <param name="design" type="data" format="tabular,tsv" label=" Comparate Design file" help="Select your Comparate Design file.  See below for correct formatting of this design file [Required]"/>
+    </inputs>
+    <outputs>
+      <collection name="split_output" type="list" label="${tool.name} on ${on_string}: Merged Comparates with Headers">
+        <discover_datasets pattern="(?P&lt;name&gt;bayesian_input_.*)" ext="tabular" sort_by="reverse_filename" directory="outputs" />
+      </collection>
+    </outputs>
+    <tests>
+        <test>
+            <param name="design" value="bayesian_input/comparate_design_file.tsv" ftype="tsv"/>
+            <param name="collection" value="merge_priors_testdata/merge_priors_to_comparate" ftype="data_collection"/>
+            <output_collection name="split_output" type="list">
+              <element name="FEATURE_ID">
+                <assert_contents>
+                  <has_text_matching expression="Merge_comparates_and_gen_headers"/>
+                </assert_contents>
+              </element>
+             </output_collection>
+        </test>
+    </tests>
+    <help><![CDATA[
+**Tool Description**
+
+The Merge Comparates and Generate Headers tool merges the comparate datasets containing the priors (generated by the Merge Priors tool) as specified in the Comparate Design File.
+New headers are created by mapping the user-specified comparate names to a general variable.
+
+**Inputs**
+
+**Collection of Merged Prior to Comparate Files [REQUIRED]**
+
+The collection of datasets containing summarized ASE Count Tables with Prior Estimates generated by the Merge Priors to Comparate tool.
+
+Example of a merged prior to comparate file in the collection (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 to be tested.
+
+**NOTE**:The Comparate Design File is created and supplied by the user. It explicitly lists the comparates that the user wants to compare.
+
+The Comparate Design File must contain the following columns, in order::
+
+    (1) Comparate_1: comparate 1 identifier (ex. W55_M)
+    (2) Comparate_2: comparate 2 identifier (ex. W55_V)
+    (3) CompID: An unique identifier that specifies the comparison (ex. W55_M_V)
+
+An example design file:
+
+    +-------------+-------------+--------+
+    | Comparate_1 | Comparate_2 | compID |
+    +=============+=============+========+
+    | W55_M       | W55_V       | W55_M_V|
+    +-------------+-------------+--------+
+
+**Outputs**
+
+    -This tool outputs the following:
+
+A TSV file containing all comparates as defined in the Comparate Design File.
+
+In the example below, the W55 Virgin and W55 Mated comparates are in a single file where c1=W55_Virgin and c2=W55_Mated. 
+
+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 |prior_c2_both       | prior_c2_g1       |  prior_c2_g2       | c2_flag_analyze  | c2_num_reps  | c2_g1_total_rep1 | c2_g2_total_rep1 | c2_both_total_rep1 | c2_flag_apn_rep1  | c2_flag_apn_rep1  | c2_APN_both_rep1 | c2_g1_total_rep2|  c2_g2_total_rep2    | c2_both_total_rep2  | c2_flag_apn_rep2  | c2_APN_total_reads_rep2 | c2_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 | 0.802196053469128  | 0.114417568427753 | 0.0833863781031191 |         1        |       2      |        691       |        519       |         5020       |         1         | 29.0734648052328  | 23.4243873865079 |      1075       |           812        |         7481        |          1        | 43.7266913990042        | 34.9168212437762  |
+    +-------------+-----------------+-------------------+--------------------+-----------------+-------------+------------------+-------------------+--------------------+------------------+-------------------------+---------------------+------------------+-------------------+--------------------+-------------------+--------------------------+------------------+--------------------+-------------------+--------------------+------------------+--------------+------------------+------------------+--------------------+-------------------+-------------------+------------------+-----------------+----------------------+---------------------+-------------------+-------------------------+-------------------+
+    | 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 | 0.866028708133971  | 0.0344497607655502| 0.0995215311004785 |         1        |       2      |         29       |         62       |          674       |         1         | 10.3878993081113  | 9.10716914470779 |        38       |           125        |          920        |          1        |  15.2470189901369       | 12.9534815250994  |
+    +-------------+-----------------+-------------------+--------------------+-----------------+-------------+------------------+-------------------+--------------------+------------------+-------------------------+---------------------+------------------+-------------------+--------------------+-------------------+--------------------------+------------------+--------------------+-------------------+--------------------+------------------+--------------+------------------+------------------+--------------------+-------------------+-------------------+------------------+-----------------+----------------------+---------------------+-------------------+-------------------------+-------------------+
+    | 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  | 0.821591948764867  | 0.108417200365965 | 0.0699908508691674 |         1        |       2      |        163       |        122       |         1112       |         1         | 89.9299663299663  | 71.5858585858586 |       237       |           134        |         1881        |          1        |  144.974410774411       | 121.086195286195  |
+    +-------------+-----------------+-------------------+--------------------+-----------------+-------------+------------------+-------------------+--------------------+------------------+-------------------------+---------------------+------------------+-------------------+--------------------+-------------------+--------------------------+------------------+--------------------+-------------------+--------------------+------------------+--------------+------------------+------------------+--------------------+-------------------+-------------------+------------------+-----------------+----------------------+---------------------+-------------------+-------------------------+-------------------+
+
+
+    ]]></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>