diff clodius.xml @ 0:8a435cbdfe3f draft

planemo upload for repository https://github.com/scottx611x/clodius-galaxy commit 66732f35a84835a50b6d3863e35e25b7291b9304-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/clodius.xml	Tue Oct 03 13:44:15 2017 -0400
@@ -0,0 +1,212 @@
+<?xml version='1.0' encoding='utf-8'?>
+
+<tool id="clodius" name="clodius" version="0.0.1">
+    <description>Clodius is a tool for breaking up large data sets into smaller tiles that can subsequently be displayed using an appropriate viewer.</description>
+     <requirements>
+        <requirement type="package" version="0.3.2">pybigwig</requirement>
+        <requirement type="package" version="0.2.19">negspy</requirement>
+        <requirement type="package" version="1.0.7">slugid</requirement>
+        <requirement type="package" version="0.6.5">clodius</requirement>
+    </requirements>
+    <command>
+    <![CDATA[
+        clodius aggregate $file_type $input_file --assembly $genome_assembly
+
+        #if $output_filename:
+          --output-file $output_filename
+        #end if
+
+        #if $file_type == "bedpe":
+            --chr1-col $chromosome_one_column
+            --from1-col $from_one_column
+            --to1-col $to_one_column
+            --chr2-col $chromosome_two_column
+            --from2-col $from_two_column
+            --to2-col $to_two_column
+        #end if
+
+        #if $file_type == "bedfile":
+          --max-per-tile $max_per_tile
+          --importance-column $importance_column
+          #if $delimiter == "tab":
+            --delimiter '\t'
+          #end if
+        #end if
+
+        #if $file_type == "bedgraph":
+            #if $chromosome_column:
+              --chromosome-col $chromosome_column
+            #end if
+            
+            #if $from_position_column:
+              --from-pos-col $from_position_column
+            #end if
+            
+            #if $to_position_column:
+              --to-pos-col $to_position_column
+            #end if
+
+            #if $value_column:
+              --value-col $value_column
+            #end if
+
+            #if $has_header:
+              --has-header
+            #end if
+
+            #if $nan_value:
+              --nan-value $nan_value
+            #end if
+        #end if
+    ]]>
+    </command>
+    <inputs>
+        <param 
+          name="chromosome_column" 
+          type="integer" 
+          label="The column number (1-based) which contains the chromosome name."
+          optional="true"/>
+        <param 
+          name="chromosome_one_column" 
+          type="integer" 
+          label="The column containing the first chromosome."
+          optional="true"/>
+        <param 
+          name="chromosome_two_column" 
+          type="integer" 
+          label="The column containing the second chromosome."
+          optional="true"/>
+        <param 
+          name="delimiter"
+          type="text"
+          optional="true"/>
+        <param 
+          name="file_type" 
+          type="text" 
+          label="Filetype to be aggregated">
+            <option value="bedpe">Bedpe-like file</option>
+            <option value="bedfile">Gene Annotation File</option>
+            <option value="bedgraph">BedGraph file</option>
+            <option value="bigwig">BigWig File</option>
+        </param>
+        <param 
+          name="from_one_column" 
+          type="integer" 
+          label="The column containing the first start position."
+          optional="true"/>
+        <param 
+          name="from_two_column" 
+          type="integer" 
+          label="The column containing the second start position."
+          optional="true"/>
+        <param 
+          name="from_position_column" 
+          type="integer" 
+          label="The column number (1-based) which contains the starting position."
+          value="2"/>
+        <param 
+          name="genome_assembly" 
+          type="text"
+          label="Genome Assembly"
+          value="hg19"/>
+        <param 
+          name="has_header" 
+          type="boolean" 
+          label="Does this file have a header that we should ignore?"
+          optional="true"/>
+        <param 
+          name="input_file" 
+          type="data" 
+          label="File to be aggregated"/>
+       <param 
+          name="importance_column" 
+          type="integer" 
+          label="The column (1-based) containing information about how important that row is. 
+          If it's absent, then use the length of the region. 
+          If the value is equal to `random`, then a random value will be used for the importance (effectively leading to random sampling)"
+          optional="true"/>
+        <param 
+          name="max_per_tile" 
+          type="integer" 
+          label="Max per tile."
+          value="100"/>
+         <param 
+          name="nan_value" 
+          type="text" 
+          label="The string to use as a NaN value."
+          optional="true"/>
+        <param 
+          name="output_filename" 
+          type="text" 
+          label="The default output file name to use. If this isn't specified, clodius will replace the current extension with something resonable."
+          optional="true"/>
+        <param 
+          name="to_one_column" 
+          type="integer" 
+          label="The column containing the first end position."
+          optional="true"/>
+        <param 
+          name="to_two_column"
+          type="integer" 
+          label="The column containing the second end position."
+          optional="true"/>
+        <param 
+          name="to_position_column" 
+          type="integer" 
+          label="The column number (1-based) which contains the ending position."
+          value="3"/>
+        <param 
+          name="value_column" 
+          type="integer" 
+          label="The column number (1-based) which contains the actual value position."
+          value="4"/>
+    </inputs>
+    <outputs>
+        <data name="output_file" />
+    </outputs>
+    <tests>
+       <test expect_num_outputs="1" expect_exit_code="0">
+          <param name="input_file" value="Rao_RepA_GM12878_Arrowhead.txt"/>
+          <param name="file_type" value="bedpe" />
+          <param name="chromosome_one_column" value="1" />
+          <param name="chromosome_two_column" value="1" />
+          <param name="from_one_column" value="2" />
+          <param name="from_two_column" value="2" />
+          <param name="to_one_column" value="3" />
+          <param name="to_two_column" value="3" />
+          <param name="output_filename" value="bedpe_test.out" />
+          <output name="output_file" file="Rao_RepA_GM12878_Arrowhead.txt.multires" />     
+        </test>
+        <test expect_num_outputs="1" expect_exit_code="0">
+          <param name="input_file" value="geneAnnotationsExonsUnions.short.bed" />
+          <param name="file_type" value="bedfile" />
+          <param name="importance_column" value="5" />
+          <param name="max_per_tile" value="20" />
+          <param name="output_filename" value="bedfile_test.out" />
+        </test> 
+        <test expect_num_outputs="1" expect_exit_code="0">
+          <param name="input_file" value="cnvs_hw.tsv" />
+          <param name="file_type" value="bedgraph" />
+          <param name="genome_assembly" value="grch37" />
+          <param name="chromosome_column" value="2" />
+          <param name="from_position_column" value="3" />
+          <param name="to_position_column" value="4" />
+          <param name="value_column" value="5" />
+          <param name="has_header" value="true" />
+          <param name="nan_value" value="NA" />
+          <param name="output_filename" value="bedgraph_test.out" />
+        </test>
+        <test expect_num_outputs="1" expect_exit_code="0">
+          <param name="input_file" value="test.bw" />
+          <param name="file_type" value="bigwig" />
+          <param name="output_filename" value="bigwig_test.out" />
+          <output name="output_file" file="test.multires.bw" lines_diff="9"/>     
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+**What it does**
+Clodius is a tool for breaking up large data sets into smaller tiles that can subsequently be displayed using an appropriate viewer.
+]]>
+    </help>
+</tool>