diff flash.xml @ 0:13e98e2709b8 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit 48012d1879395ecf1b4e6cd962f325c372164a33

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/flash.xml	Tue Sep 26 16:42:09 2017 -0400
@@ -0,0 +1,89 @@
+<?xml version="1.0"?>
+<tool id="flash" name="FLASH" version="1.2.11">
+    <description>adjust length of short reads</description>
+    <requirements>
+        <requirement type="package" version="1.2.11">flash</requirement>
+    </requirements>
+    <version_command>flash --version | head -n 1</version_command>
+    <command detect_errors="aggressive">
+        <![CDATA[
+            flash --threads=\${GALAXY_SLOTS:-1}
+                -m $min_overlap
+                -M $max_overlap
+                -x $max_mismatch_density
+                $allow_outies
+                '$forward' '$reverse'
+        ]]>
+    </command>
+    <inputs>
+        <param format="fastq" name="forward" type="data" label="Forward reads" />
+        <param format="fastq" name="reverse" type="data" label="Reverse reads" />
+        <param name="min_overlap" argument="--min-overlap" type="integer" optional="true" value="10" label="Minimum overlap" help="The minimum required overlap length between two reads to provide a confident overlap." />
+        <param name="max_overlap" argument="--max-overlap" type="integer" optional="true" value="65" label="Maximum overlap" help="Maximum overlap length expected in approximately 90% of read pairs. Overlaps longer than the maximum overlap parameter are still considered as good overlaps, but the mismatch density is calculated over the first max_overlap bases in the overlapped region rather than the entire overlap." />
+        <param name="max_mismatch_density" argument="--max-mismatch-density" type="float" optional="true" value="0.25" label="Maximum mismatch density" help="Maximum allowed ratio between the number of mismatched base pairs and the overlap length. Two reads will not be combined with a given overlap if that overlap results in a mismatched base density higher than this value." />
+        <param name="allow_outies" argument="--allow-outies" type="boolean" truevalue="--allow-outies" falsevalue="" checked="false" label="Combine read pairs in both orientations" help="FLASH uses the same parameters when trying each orientation. If a read pair can be combined in either orientation, the better-fitting one will be chosen using the same scoring algorithm that FLASH normally uses." />
+    </inputs>
+    <outputs>
+        <data format="fastq" name="merged_reads" from_work_dir="out.extendedFrags.fastq" label="${tool.name} on ${on_string}: Merged reads" />
+        <data format="fastq" name="unmerged_reads_f" from_work_dir="out.notCombined_1.fastq" label="${tool.name} on ${on_string}: Unmerged forward reads" />
+        <data format="fastq" name="unmerged_reads_r" from_work_dir="out.notCombined_2.fastq" label="${tool.name} on ${on_string}: Unmerged reverse reads" />
+        <data format="tabular" name="hist" from_work_dir="out.hist" label="${tool.name} on ${on_string}: Unmerged reads tabular histogram" />
+        <data format="txt" name="histogram" from_work_dir="out.histogram" label="${tool.name} on ${on_string}: Unmerged reads histogram" />
+        <data format="tabular" name="hist_in" from_work_dir="out.hist.innie" label="${tool.name} on ${on_string}: Unmerged reads tabular histogram (in)" >
+            <filter>allow_outies</filter>
+        </data>
+        <data format="tabular" name="hist_out" from_work_dir="out.hist.outie" label="${tool.name} on ${on_string}: Unmerged reads tabular histogram (out)" >
+            <filter>allow_outies</filter>
+        </data>
+        <data format="txt" name="histogram_in" from_work_dir="out.histogram.innie" label="${tool.name} on ${on_string}: Unmerged reads histogram (in)" >
+            <filter>allow_outies</filter>
+        </data>
+        <data format="txt" name="histogram_out" from_work_dir="out.histogram.outie" label="${tool.name} on ${on_string}: Unmerged reads histogram (out)" >
+            <filter>allow_outies</filter>
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <param name="forward" value="flash_forward_in1.fastq" />
+            <param name="reverse" value="flash_reverse_in1.fastq" />
+            <output name="merged_reads" file="flash_merged_out1.fastq" />
+            <output name="unmerged_reads_f" file="flash_unmerged_f_out1.fastq" />
+            <output name="unmerged_reads_r" file="flash_unmerged_r_out1.fastq" />
+            <output name="hist" file="flash_hist_out1.tabular" />
+            <output name="histogram" file="flash_hist_out1.txt" />
+        </test>
+        <test>
+            <param name="forward" value="flash_forward_in2.fastq" />
+            <param name="reverse" value="flash_reverse_in2.fastq" />
+            <param name="allow_outies" value="true" />
+            <output name="merged_reads" file="flash_merged_out2.fastq" />
+            <output name="unmerged_reads_f" file="flash_unmerged_f_out2.fastq" />
+            <output name="unmerged_reads_r" file="flash_unmerged_r_out2.fastq" />
+            <output name="hist" file="flash_hist_out2.tabular" />
+            <output name="histogram" file="flash_hist_out2.txt" />
+            <output name="hist_in" file="flash_hist_in_out2.tabular" />
+            <output name="histogram_in" file="flash_hist_in_out2.txt" />
+            <output name="hist_out" file="flash_hist_out_out2.tabular" />
+            <output name="histogram_out" file="flash_hist_out_out2.txt" />
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+FLASH (Fast Length Adjustment of SHort reads) is an accurate and fast tool
+to merge paired-end reads that were generated from DNA fragments whose
+lengths are shorter than twice the length of reads.  Merged read pairs result
+in unpaired longer reads, which are generally more desired in genome
+assembly and genome analysis processes.
+
+Briefly, the FLASH algorithm considers all possible overlaps at or above a
+minimum length between the reads in a pair and chooses the overlap that
+results in the lowest mismatch density (proportion of mismatched bases in
+the overlapped region).  Ties between multiple overlaps are broken by
+considering quality scores at mismatch sites.  When building the merged
+sequence, FLASH computes a consensus sequence in the overlapped region.
+]]>
+    </help>
+    <citations>
+        <citation type="doi">10.1093/bioinformatics/btr507</citation>
+    </citations>
+</tool>
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