diff crosscontamination_barcode_filter.xml @ 2:e20001675838 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 82a0fd493f5866b3ef65019709ae5c865998f802

--- a/crosscontamination_barcode_filter.xml	Mon Jun 03 14:54:55 2019 -0400
+++ b/crosscontamination_barcode_filter.xml	Wed Jun 12 04:57:52 2019 -0400
@@ -1,7 +1,7 @@
 <tool id="crosscontamination_barcode_filter" name="Cross-contamination Barcode Filter" version="@VERSION@">
     <description>for use in plate-based barcoded analyses</description>
     <macros>
-        <token name="@VERSION@">0.2</token>
+        <token name="@VERSION@">0.3</token>
         <macro name="sanitize_batch">
             <sanitizer invalid_char="">
                 <valid initial="string.digits">
@@ -85,6 +85,7 @@
 #end if
 regex.extract = '$advanced.regex_extract'
 regex.display = '$advanced.regex_display'
+sort.cells = as.logical('$advanced.sort_sizes')
 out.pdf = '$out_plots'
 out.table = '$out_table'
 ]]>
@@ -115,13 +116,14 @@
                 </repeat>
             </when>
         </conditional>
-        <section name="advanced" expanded="false" title="RegEx Parameters" >
+        <section name="advanced" expanded="false" title="Advanced Parameters" >
             <param name="regex_extract" type="text" value=".*P(\\d)_B(\\d)_([ACTG]+)" label="RegEx to extract Plate, Batch, and Barcodes from headers" >
                 <expand macro="sanitize_regex" />
             </param>
             <param name="regex_display" type="text" value="P\\1_B\\2_\\3" label="RegEx to replace Plate, Batch, and Barcodes from headers" >
                 <expand macro="sanitize_regex" />
             </param>
+            <param name="sort_sizes" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Sort Cells by Library Size" />
         </section>
     </inputs>
     <outputs>
@@ -165,12 +167,44 @@
             <output name="out_plots" value="out.pdf" compare="sim_size" />
             <output name="out_table" value="out.table" />
         </test>
+        <test><!-- 12 Batch test -->
+            <param name="input_table" value="b12.matrix" />
+            <param name="input_barcodes" value="celseq_barcodes.192.raw" />
+            <conditional name="inbuilt_spec" >
+                <param name="select_use" value="custom" />
+                <repeat name="barcode_format" >
+                    <param name="range_start" value="1"/>
+                    <param name="range_end" value="96" />
+                    <param name="batches" value="1,3,5,7,9,11" />
+                </repeat>
+                <repeat name="barcode_format" >
+                    <param name="range_start" value="97"/>
+                    <param name="range_end" value="192" />
+                    <param name="batches" value="2,4,6,8,10,12" />
+                </repeat>
+                <repeat name="plate_format" >
+                    <param name="plate" value="1" />
+                    <param name="batches" value="1,2,3,4" />
+                </repeat>
+                <repeat name="plate_format" >
+                    <param name="plate" value="2" />
+                    <param name="batches" value="5,6,7,8" />
+                </repeat>
+                <repeat name="plate_format" >
+                    <param name="plate" value="3" />
+                    <param name="batches" value="9,10,11,12" />
+                </repeat>
+            </conditional>
+            <output name="out_plots" value="b12.pdf" compare="sim_size" />
+            <output name="out_table" value="b12.table" />
+        </test>
     </tests>
     <help><![CDATA[
 Cross-contamination Filter Plot
 ###################################
 
 For a set of barcodes and an experimental setup that uses a subset of these barcodes for each batch, this tool compares each batch against the full range of barcodes in order to determine whether any cross-contamination between batches has occured.
+*Note -- Do not reuse batch numbering across plates!*
 
 If a significant number of transcripts are shown in a batch for cell barcodes that were not designed for that batch, then this tool will show that. In the below plot, we can see that there is no significant cross-contamination taking place (pre-filter), and so we can filter out the false barcodes (post-filter).