diff tag_pileup_frequency.xml @ 0:fa82c3c9ced3 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tag_pileup_frequency.xml	Tue May 17 14:15:39 2016 -0400
@@ -0,0 +1,114 @@
+<tool id="tag_pileup_frequency" name="Tag pileup frequency" version="1.0.0">
+    <description></description>
+    <requirements>
+        <requirement type="package" version="8.0.45">java-jdk</requirement>
+    </requirements>
+    <command>
+        <![CDATA[
+            mkdir -p output &&
+            ln -f -s "${input1.metadata.bam_index}" "${input1}.bai" &&
+            java -jar $__tool_directory__/TagPileup.jar
+            -b "$input1"
+            -i "${input1}.bai"
+            -c "$input2"
+            -s $tag_shift
+            -n $bin_size
+            -e $tags_equal
+            -r $reads
+            -p $proper_pe
+            -a $combine_strands
+            -t "\${GALAXY_SLOTS:-4}"
+            -w $composite_smoothing_window
+            -m "true"
+            -x "$output1"
+            -h $output_heatmap
+            #if str($output_heatmap) == "true":
+                -o output
+            #end if
+            1>/dev/null
+        ]]>
+    </command>
+    <inputs>
+        <param name="input1" type="data" format="bam" label="BAM file" />
+        <param name="input2" type="data" format="bed" label="Bed file" />
+        <param name="tag_shift" type="integer" value="0" min="0" label="5' to 3' Tag Shift (bp)" />
+        <param name="bin_size" type="integer" value="1" min="1" label="Bin Size (bp)" />
+        <param  name="tags_equal" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Set Tags to be equal?" />
+        <param  name="reads" type="select" label="Reads to examine" help="Selecting combined requires paired-end BAM input">
+            <option value="0" selected="True">Read1</option>
+            <option value="1">Read2</option>
+            <option value="2">combined</option>
+        </param>
+        <param  name="proper_pe" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Require proper PE?" help="Requires paired-end BAM input"/>
+        <param  name="combine_strands" type="select" label="Combine strands?">
+            <option value="0" selected="True">No</option>
+            <option value="1">Yes</option>
+        </param>
+        <param name="composite_smoothing_window" type="integer" value="0" min="0" label="Composite smoothing window (bp)" />
+        <param name="output_heatmap" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Output frequencies heatmap?" />
+    </inputs>
+    <outputs>
+        <collection name="heatmaps" type="list" label="Heatmap frequencies: ${tool.name} on ${on_string}">
+            <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="output" ext="tabular" visible="false" />
+            <filter>output_heatmap == true</filter>
+        </collection>
+        <data name="output1" format="tabular"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input1" value="input.bam" ftype="bam"/>
+            <param name="input2" value="input.bed" ftype="bed"/>
+            <param name="tag_shift" value="0" />
+            <param name="bin_size" value="1" />
+            <param name="tags_equal" value="false" />
+            <param name="reads" value="0" />
+            <param name="proper_pe" value="false" />
+            <param name="combine_strands" value="0" />
+            <param name="composite_smoothing_window" value="0" />
+            <param name="output_heatmap" value="true" />
+            <output name="output1" file="output1.tabular" ftype="tabular"/>
+            <output_collection name="heatmaps" type="list">
+                <element name="dataset_2_dataset_1_read1_anti.tabular" file="input2_input1_read1_anti.tabular" ftype="tabular" compare="contains"/>
+                <element name="dataset_2_dataset_1_read1_sense.tabular" file="input2_input1_read1_sense.tabular" ftype="tabular" compare="contains"/>
+            </output_collection>
+        </test>
+    </tests>
+    <help>
+
+**What it does**
+
+Generates a frequency pileup of the 5' ends of aligned reads in a BAM file relative to reference points in a BED file.
+
+-----
+
+**Options**
+
+**Global transformations**
+
+ - **5' to 3' tag shift (bp)** - moves all tags from the 5' to the 3' direction given a specified distance in base pairs.
+ - **Bin Size (bp)** - bins tags together into specified size, useful for lower resolution data or for especially wide reference windows.
+ - **Set Tags to be equal** - standardizes tag count to be equal to genome size, useful for replicate comparisons.
+
+**Read parameters**
+
+ - **Reads to Examine** - output data for Read1, Read2, or combined (only for paired end BAM files).
+ - **Require Proper PE** - require output reads to be properly paired (only for paired end BAM files).
+ - **Combine Strands** - examine reads on a forward/reverse basis (strand separate) or ignoring read orientation (strand combined).
+
+**Run parameters**
+
+ - **Composite smoothing window (bp)** - sliding window to smooth composite frequencies.
+ - **Output frequencies for heatmap** - generate an additional dataset collection containing frequencies that can be used to generate a heatmap plot.
+
+    </help>
+    <citations>
+        <citation type="bibtex">
+            @unpublished{None,
+            author = {Lai, William},
+            title = {None},
+            year = {None},
+            eprint = {None},
+            url = {http://www.huck.psu.edu/content/research/independent-centers-excellence/center-for-eukaryotic-gene-regulation}
+        }</citation>
+    </citations>
+</tool>