diff pear.xml @ 0:581e52f03c5d draft

Imported from capsule None

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pear.xml	Wed May 20 14:59:50 2015 -0400
@@ -0,0 +1,160 @@
+<tool id="iuc_pear" name="Pear" version="0.9.6.0">
+    <description>Paired-End read merger</description>
+    <!--<version_command>bismark version</version_command>-->
+    <requirements>
+        <requirement type="package" version="0.9.6">pear</requirement>
+    </requirements>
+    <stdio>
+        <exit_code range="1:" />
+        <exit_code range=":-1" />
+        <regex match="Error:" />
+        <regex match="Exception:" />
+    </stdio>
+    <command>
+<![CDATA[
+    pear
+        #if str( $library.type ) == "paired":
+            -f "$library.forward"
+            -r "$library.reverse"
+        #else
+            ## prepare collection
+            -f $library.input_collection.forward
+            -r $library.input_collection.reverse
+        #end if
+
+        --output pear
+        --p-value $pvalue
+        --min-overlap $min_overlap
+        #if int($max_assembly_length) > 0:
+            --max-asm-length $max_assembly_length
+        #end if
+        --min-asm-length $min_assembly_length
+        --min-trim-length $min_trim_length
+        --quality-theshold $quality_threshold
+        --max-uncalled-base $max_uncalled_base
+        --test-method $test_method
+        --empirical-freqs $empirical_freqs
+        -j "\${GALAXY_SLOTS:-8}"
+        --score-method $score_method
+        --cap $cap
+        $nbase
+]]>
+    </command>
+    <inputs>
+        <conditional name="library">
+            <param name="type" type="select" label="Dataset type">
+              <option value="paired">Paired-end</option>
+              <option value="paired_collection">Paired-end Dataset Collection</option>
+            </param>
+            <when value="paired">
+                <param name="forward" type="data" format="fastqillumina, fastqsanger, fastq"
+                    label="Name of file that contains the forward paired-end reads" help="-f" />
+                <param name="reverse" type="data" format="fastqillumina, fastqsanger, fastq"
+                    label="Name of file that contains the reverse paired-end reads" help="-r" />
+            </when>
+            <when value="paired_collection">
+                <param name="input_collection" format="fastqillumina, fastqsanger, fastq"
+                    type="data_collection" collection_type="paired"
+                    label="FASTQ Paired Dataset" help="Nucleotide-space: Must have Sanger-scaled quality values with ASCII offset 33. (-f and -r)" />
+            </when>
+        </conditional>
+
+        <!-- optional -->
+        <param name="pvalue" type="float" value="0.01" min="0" optional="True" max="1" label="Specify a p-value for the statistical test"
+            help="If the computed p-value of a possible assembly exceeds the specified p-value then the paired-end read will not be assembled. Setting 1.0 disables the test. (--p-value)" />
+
+        <param name="min_overlap" type="integer" value="10" optional="True" label="Minimum overlap size"
+            help="The minimum overlap may be set to 1 when the statistical test is used. However, further restricting the minimum overlap size to a proper value may reduce false-positive assembles. (--min-overlap)" />
+
+        <param name="max_assembly_length" type="integer" value="0" optional="True" label="Maximum possible length of the assembled sequences"
+            help="Setting this value to 0 disables the restriction and assembled sequences may be arbitrary long. (--max-assembly-length)" />
+
+        <param name="min_assembly_length" type="integer" value="50" optional="True" label="Minimum possible length of the assembled sequences"
+            help="Setting this value to 0 disables the restriction and assembled sequences may be arbitrary short. (--min-assembly-length)" />
+
+        <param name="min_trim_length" type="integer" value="1" optional="True" label="Minimum length of reads after trimming the low quality part"
+            help="See option -q. (--min-trim-length)" />
+
+        <param name="quality_threshold" type="integer" value="0" optional="True" label="Quality score threshold for trimming the low quality part of a read"
+                help="If the quality scores of two consecutive bases are strictly less than the specified threshold, the rest of the read will be trimmed. (--quality-threshold)" />
+
+        <param name="max_uncalled_base" type="float" value="1.0" min="0" optional="True" max="1" label="Maximal proportion of uncalled bases in a read"
+            help="Setting this value to 0 will cause PEAR to discard all reads containing uncalled bases. The other extreme setting is 1 which causes PEAR to process all reads independent on the number of uncalled bases. (--max-uncalled-base)" />
+
+        <param name="cap" type="integer" value="40" optional="True" label="Specify  the upper bound for the resulting quality score"
+            help="If set to zero, capping is disabled. (--cap)" />
+
+        <param name="test_method" type="select" label="Type of statistical test" help="(--test-method)">
+            <option value="1" selected="True">Given the minimum allowed overlap, test using the highest OES (1)</option>
+            <option value="2">Use the acceptance probability (2)</option>
+        </param>
+
+        <param name="empirical_freqs" type="boolean" truevalue="-e" falsevalue="" checked="false"
+            label="Disable empirical base frequencies" help="(--empirical-freqs)" />
+        <param name="nbase" type="boolean" truevalue="--nbase" falsevalue="" checked="false"
+            label="Use N base if uncertain" help="When  merging a base-pair that consists of two non-equal bases out of which none is degenerate, set the merged base to N and use the highest quality score of the two bases. (--nbase)" />
+
+        <param name="score_method" type="select" label="Scoring method" help="(--score-method)">
+            <option value="1">OES with +1 for match and -1 for mismatch</option>
+            <option value="2" selected="True">Assembly score (AS) use +1 for match and -1 for mismatch multiplied by base quality scores</option>
+            <option value="3">Ignore quality scores and use +1 for a match and -1 for a mismatch</option>
+        </param>
+
+        <param name="outputs" type="select" display="checkboxes" optional="False" multiple="True" label="Output files">
+            <option value="assembled" selected="True">Assembled reads</option>
+            <option value="forward">Forward unassembled reads</option>
+            <option value="reverse">Reverse unassembled reads</option>
+            <option value="discarded">Discarded reads</option>
+        </param>
+    </inputs>
+    <outputs>
+        <data format="fastq" name="assembled_reads" from_work_dir="pear.assembled.fastq" label="${tool.name} on ${on_string}: Assembled reads">
+            <filter>'assembled' in outputs</filter>
+        </data>
+        <data format="fastq" name="unassembled_forward_reads" from_work_dir="pear.unassembled.forward.fastq" label="${tool.name} on ${on_string}: Unassembled forward reads">
+            <filter>'forward' in outputs</filter>
+        </data>
+        <data format="fastq" name="unassembled_reverse_reads" from_work_dir="pear.unassembled.reverse.fastq" label="${tool.name} on ${on_string}: Unassembled reverse reads">
+            <filter>'reverse' in outputs</filter>
+        </data>
+        <data format="fastq" name="discarded_reads" from_work_dir="pear.discarded.fastq" label="${tool.name} on ${on_string}: Discarded reads">
+            <filter>'discarded' in outputs</filter>
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <param name="forward" value="forward.fastq" ftype="fastq" />
+            <param name="reverse" value="reverse.fastq" ftype="fastq" />
+            <param name="min_overlap" value="10" />
+            <param name="min_assembly_length" value="50" />
+            <param name="cap" value="0" />
+            <param name="outputs" value="assembled,forward" />
+            <output name="assembled_reads" file="pear_assembled_results1.fastq" ftype="fastq"/>
+            <output name="unassembled_forward_reads" file="pear_unassembled_forward_results1.fastq" ftype="fastq"/>
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+
+
+**What it does**
+
+PEAR_ is an ultrafast, memory-efficient and highly accurate pair-end read merger.
+PEAR evaluates all possible paired-end read overlaps and without requiring the target fragment
+size as input. In addition, it implements a statistical test for minimizing false-positive results.
+Together with a highly optimized implementation, it can merge millions of paired end reads within a couple of minutes
+on a standard desktop computer.
+
+For more information please look at the documentation_ and `github repository`_.
+
+.. _PEAR: http://sco.h-its.org/exelixis/web/software/pear/
+.. _documentation: http://sco.h-its.org/exelixis/web/software/pear/doc.html
+.. _github repository: https://github.com/xflouris/PEAR
+
+
+]]>
+  </help>
+  <citations>
+      <citation type="doi">10.1093/bioinformatics/btt593</citation>
+  </citations>
+</tool>