--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/size_histogram.xml	Tue Jul 11 11:44:36 2017 -0400
@@ -0,0 +1,168 @@
+<tool id="artbio_size_histogram" name="Generate read size histograms" version="1.0.0">
+    <description>from alignment files</description>
+    <requirements>
+        <requirement type="package" version="1.2.0=py27_0">bowtie</requirement>
+        <requirement type="package" version="0.11.2.1=py27_0">pysam</requirement>
+        <requirement type="package" version="1.9.3">numpy</requirement>
+        <requirement type="package" version="1.3.2=r3.3.2_0">r-optparse</requirement>
+        <requirement type="package" version="0.6_28=r3.3.2_0">r-latticeextra</requirement>
+        <requirement type="package" version="2.2.1=r3.3.2_0">r-gridextra</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        python '$__tool_directory__'/size_histogram.py
+        #if $refGenomeSource.genomeSource == "history":
+            --reference_fasta  ## sys.argv[2]
+            '$refGenomeSource.ownFile' ## index source
+        #else:
+            #silent reference= filter( lambda x: str( x[0] ) == str( $refGenomeSource.series[0].input.dbkey ), $__app__.tool_data_tables[ 'bowtie_indexes' ].get_fields() )[0][-1]
+            --reference_bowtie_index
+            '$reference'
+        #end if
+        --output_size_distribution
+        '$size_distribution_dataframe'
+        --minquery
+        $minquery
+        --maxquery
+        $maxquery
+        --input
+        #for $i in $refGenomeSource.series
+            '$i.input'
+        #end for
+        --ext
+        #for $i in $refGenomeSource.series
+            '$i.input.ext'
+        #end for
+        --label
+        #for $i in $refGenomeSource.series
+            "$i.input.element_identifier"
+        #end for
+        #if $gff:
+            --gff '$gff'
+        #end if
+        #if $global.value == 'yes':
+            --global_size
+        #end if
+        #if $collapsestrands.value == 'yes':
+            --collapse
+        #end if
+        --normalization_factor
+        #for $i in $refGenomeSource.series
+            $i.norm
+        #end for
+        &&
+        Rscript '$__tool_directory__'/size_histogram.r
+            --global '$global'
+            --size_distribution_tab '$size_distribution_dataframe'
+            --size_distribution_pdf '$size_PDF'
+            --title '$title'
+            --ylabel '$ylabel'
+            --yrange '$yrange'
+            --rows_per_page '$rows_per_page'
+    ]]></command>
+    <inputs>
+        <conditional name="refGenomeSource">
+            <param name="genomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options">
+                <option value="indexed">Use a built-in index</option>
+                <option value="history">Use one from the history</option>
+            </param>
+            <when value="indexed">
+                <repeat name="series" title="Add alignment files">
+                    <param name="input" type="data" label="Select multiple alignments to parse" format="tabular,sam,bam">
+                        <validator type="dataset_metadata_in_data_table" table_name="bowtie_indexes" metadata_name="dbkey" metadata_column="0" message="database not set for this bowtie output. Select the database(=genome used for matching) manually, or select a reference fasta from your history."/>
+                    </param>
+                    <param name="norm" type="float" value="1" label="Indicate a normalization factor to compare multiple aligments"/>
+                </repeat>
+            </when>
+            <when value="history">
+                <param name="ownFile" type="data" format="fasta" label="Select a fasta file, to serve as index reference" />
+                <repeat name="series" title="Add alignment files">
+                    <param name="input" type="data" label="Select multiple alignments to parse" format="tabular,sam,bam"/>
+                    <param name="norm" type="float" value="1" label="Indicate a normalization factor to compare multiple aligments"/>
+                </repeat>
+            </when>
+        </conditional>
+        <param name="gff" type="data" format="gff,gff3" optional="true" label="Optional: select a GFF to investigate regions of interest" help="GFF must match genome build"/>
+        <!-- <validator type="dataset_metadata_in_data_table" table_name="bowtie_indexes" metadata_name="dbkey" metadata_column="0" message="GFF database and alignment file databse do not match!"/> -->
+        <param name="global" type="select" label="Generate size distribution for each item, or generate a global alignment">
+            <option value="no">for each item</option>
+            <option value="yes">global</option>
+        </param>
+        <param name="collapsestrands" type="select" label="Whether + and - reads should be collapsed or not">
+            <option value="no">Do not collapse</option>
+            <option value="yes">Collapse + and - reads</option>
+        </param>
+        <param name="minquery" type="integer" size="3" value="18" label="Min size of reads to plot" help="'15' = 15 nucleotides"/>
+        <param name="maxquery" type="integer" size="3" value="28" label="Max size of reads to plot" help="'30' = 30 nucleotides"/>
+        <param name="title" type="text" size="15" value="Size distribution" label="Main Titles"/>
+        <param name="xlabel" type="text" size="15" value="Size in nucleotides" label="x axis label"/>
+        <param name="ylabel" type="text" size="15" value="Number of reads" label="y axis label"/>
+        <param name="yrange" type="integer" size="3" value="0" label="y axis range for size distributions. 0 means auto-scaling."/>
+        <param name="rows_per_page" type="text" size="9" value="8" label="How many items to display per page?">
+            <validator type="in_range" min="6" max="20" message="Select between 6 and 20 rows, as the readability will suffer otherwise."/>
+        </param>
+    </inputs>
+
+    <outputs>
+        <data format="tabular" name="size_distribution_dataframe" label="Size_distribution_dataframe.tab"/>
+        <data format="pdf" name="size_PDF" label="Size_distribution.pdf"/>
+    </outputs>
+
+<help>
+
+**What it does**
+
+Takes one or more alignment files (BAM, SAM or tabular bowtie output) as input and produces a histogram of read sizes,
+where by default for each "chromosome" a histogram of read sizes is drawn.
+Reads that map in sense are on the top (red), reads that map antisense are on the bottom (blue).
+
+
+.. class:: warningmark
+
+'''TIP''' The input data can be produced using the sRbowtie tool.
+
+----
+
+'''Example'''
+
+Query sequence::
+For a SAM file as the following:
+
+  5	16	2L_79	24393	255	17M	*	0	0	CCTTCATCTTTTTTTTT	IIIIIIIIIIIIIIIII	XA:i:0	MD:Z:17	NM:i:0
+
+  11	0	2R_1	12675	255	21M	*	0	0	AAAAAAAACGCGTCCTTGTGC	IIIIIIIIIIIIIIIIIIIII	XA:i:0	MD:Z:21	NM:i:0
+
+  2	16	2L_5	669	255	23M	*	0	0	TGTTGCTGCATTTCTTTTTTTTT	IIIIIIIIIIIIIIIIIIIIIII	XA:i:0	MD:Z:23	NM:i:0
+
+produce a plot like this:
+
+----
+
+.. image:: static/images/size_histogram.png
+    :height: 800
+    :width: 500
+
+</help>
+    <tests>
+        <test>
+            <param name="genomeSource" value="history" />
+            <param name="ownFile" value="transposons.fasta" ftype="fasta" />
+            <param name="series_0|input" value="sample1.srbowtie_out" ftype="tabular"/>
+            <param name="series_0|norm" value="1" />
+            <param name="series_1|input" value="sample2.srbowtie_out" ftype="tabular"/>
+            <param name="series_1|norm" value="1" />
+            <param name="series_2|input" value="sample3.srbowtie_out" ftype="tabular"/>
+            <param name="series_2|norm" value="1" />
+            <param name="global" value="no" />
+            <param name="collapsestrands" value="no" />
+            <param name="minquery" value="18"/>
+            <param name="maxquery" value="30"/>
+            <param name="title" value="Size distribution"/>
+            <param name="xlabel" value="Size in nucleotides"/>
+            <param name="ylabel" value="Number of reads"/>
+            <param name="rows_per_page" value="10"/>
+            <output name="size_distribution_dataframe" ftype="tabular" file="Size_distribution_dataframe.tab" />
+            <output name="size_PDF" ftype="pdf" file="Size_distribution.pdf" />
+        </test>
+    </tests>
+</tool>
+