--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pear.xml	Wed Feb 11 07:52:43 2015 -0500
@@ -0,0 +1,204 @@
+<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
+        -f $forward
+        -r $reverse
+        --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>
+        <param name="forward" type="data" format="fastqillumina, fastqsanger, fastq"
+            label="Specify the name of file that contains the forward paired-end reads" help="-f" />
+        <param name="reverse" type="data" format="fastqillumina, fastqsanger, fastq"
+            label="Specify the name of file that contains the reverse paired-end reads" help="-r" />
+
+        <!-- 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="Specify the 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="Specify the 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="Specify the 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="Specify the 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="Specify the 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="Specify the 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="Specify the 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="Specify the 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" 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>
+
+            <validator type="no_options" message="Please select at least one output file." />
+        </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.
+It is fully parallelized and can run with as low as just a few kilobytes of memory.
+
+
+**Parameters**
+
+
+Standard (mandatory):
+  -f, --forward-fastq         <str>     Forward paired-end FASTQ file.
+  -r, --reverse-fastq         <str>     Reverse paired-end FASTQ file.
+
+Optional:
+  -p, --p-value               <float>   Specify  a p-value for the statistical test. If the computed
+                                        p-value of a possible assembly exceeds the specified p-value
+                                        then  paired-end  read  will not be assembled. Valid options
+                                        are: 0.0001, 0.001, 0.01, 0.05 and 1.0. Setting 1.0 disables
+                                        the test. (default: 0.01)
+  -v, --min-overlap           <int>     Specify the minimum overlap size. 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. (default: 10)
+  -m, --max-assembly-length   <int>     Specify   the  maximum  possible  length  of  the  assembled
+                                        sequences.  Setting this value to 0 disables the restriction
+                                        and assembled sequences may be arbitrary long. (default: 0)
+  -n, --min-assembly-length   <int>     Specify   the  minimum  possible  length  of  the  assembled
+                                        sequences.  Setting this value to 0 disables the restriction
+                                        and  assembled  sequences  may be arbitrary short. (default:
+                                        50)
+  -t, --min-trim-length       <int>     Specify  the  minimum length of reads after trimming the low
+                                        quality part (see option -q). (default: 1)
+  -q, --quality-threshold     <int>     Specify  the  quality  score  threshold for trimming the low
+                                        quality  part  of  a  read.  If  the  quality  scores of two
+                                        consecutive  bases  are  strictly  less  than  the specified
+                                        threshold,  the  rest of the read will be trimmed. (default:
+                                        0)
+  -u, --max-uncalled-base     <float>   Specify  the maximal proportion of uncalled bases in a read.
+                                        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. (default: 1)
+  -g, --test-method           <int>     Specify  the  type  of  statistical  test.  Two  options are
+                                        available. (default: 1)
+                                        1: Given the minimum allowed overlap, test using the highest
+                                        OES. Note that due to its discrete nature, this test usually
+                                        yields  a lower p-value for the assembled read than the cut-
+                                        off  (specified  by -p). For example, setting the cut-off to
+                                        0.05  using  this  test,  the  assembled reads might have an
+                                        actual p-value of 0.02.
+
+                                        2. Use the acceptance probability (m.a.p). This test methods
+                                        computes  the same probability as test method 1. However, it
+                                        assumes  that  the  minimal  overlap is the observed overlap
+                                        with  the  highest  OES, instead of the one specified by -v.
+                                        Therefore,  this  is  not  a  valid statistical test and the
+                                        'p-value'  is  in fact the maximal probability for accepting
+                                        the assembly. Nevertheless, we observed in practice that for
+                                        the case the actual overlap sizes are relatively small, test
+                                        2  can  correctly  assemble  more  reads  with only slightly
+                                        higher false-positive rate.
+  -e, --empirical-freqs                 Disable  empirical base frequencies. (default: use empirical
+                                        base frequencies)
+  -s, --score-method          <int>     Specify the scoring method. (default: 2)
+                                        1. OES with +1 for match and -1 for mismatch.
+                                        2: Assembly score (AS). Use +1 for match and -1 for mismatch
+                                        multiplied by base quality scores.
+                                        3: Ignore quality scores and use +1 for a match and -1 for a
+                                        mismatch.
+  -c, --cap                   <int>     Specify  the upper bound for the resulting quality score. If
+                                        set to zero, capping is disabled. (default: 40)
+  -z, --nbase                           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
+
+
+
+
+]]>
+  </help>
+  <citations>
+      <citation type="doi">10.1093/bioinformatics/btt593</citation>
+  </citations>
+</tool>