--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/trim_galore.xml	Wed Oct 07 08:39:59 2015 -0400
@@ -0,0 +1,372 @@
+<tool id="trim_galore" name="Trim Galore!" version="0.4.0">
+    <!-- Wrapper compatible with Trim Galore! version 0.4 -->
+    <description>adaptive quality and adapter trimmer</description>
+    <macros>
+        <macro name="adapter_trimming">
+            <conditional name="trimming">
+                <param name="trimming_select" type="select" label="Trimming reads?">
+                    <option value="">Automatic detection</option>
+                    <option value="--illumina">Illumina universal</option>
+                    <option value="--nextera">Nextera transposase</option>
+                    <option value="--small_rna">Illumina small RNA adapters</option>
+                    <option value="user">User defined adapter trimming</option>
+                </param>
+                <when value="auto"/>
+                <when value="--illumina"/>
+                <when value="--nextera"/>
+                <when value="--small_rna"/>
+                <when value="user">
+                    <param name="adapter" type="text" value="AGATCGGAAGAGC" label="Adapter sequence to be trimmed off">
+                        <validator type="regex" message="Adapter sequence must contain DNA characters only (A,C,T,G or N)">^[ACTGNactgn]*$</validator>
+                    </param>
+                    <yield/>
+                </when>
+            </conditional>
+        </macro>
+        <macro name="paired_adapter_trimming">
+
+            <expand macro="adapter_trimming">
+                <param name="adapter2" type="text" optional="True" value="" label="Adapter sequence to be trimmed off read 2">
+                    <validator type="regex" message="Adapter sequence must contain DNA characters only (A,C,T,G or N)">^[ACTGNactgn]*$</validator>
+                </param>
+            </expand>
+            <param name="trim1" type="boolean" truevalue="--trim1" falsevalue="" checked="False" label="Trims 1 bp off every read from its 3' end." help="" />
+            <param name="three_prime_clip_R1" type="integer" value="" optional="True" label="Remove N bp from the 3' end of read 1">
+                <help>Instructs Trim Galore! to remove N bp from the 3' end of read 1 after adapter/quality trimming has been performed.
+                    This may remove some unwanted bias from the 3' end that is not directly related to adapter sequence or basecall quality.
+                    (--three_prime_clip_R1)</help>
+            </param>
+            <param name="three_prime_clip_R2" type="integer" value="" optional="True" label="Remove N bp from the 3' end of read 1">
+                <help>Instructs Trim Galore! to remove N bp from the 3' end of read 2 after
+                    adapter/quality trimming has been performed. This may remove some unwanted bias from
+                    the 3' end that is not directly related to adapter sequence or basecall quality. (--three_prime_clip_R2)</help>
+            </param>
+        </macro>
+    </macros>
+    <requirements>
+        <requirement type="package" version="1.8">cutadapt</requirement>
+    </requirements>
+    <version_command interpreter="perl">trim_galore --version</version_command>
+    <command>
+<![CDATA[
+
+        ## trim_galore removes .fastq and .fq file extensions of input files.
+        ## This is essential if Galaxy provides links to files (with real extensions)
+        ## but that behaviour is causing an inconsistency in output filenaming.
+        ## We work around this by linking every file to cwd without file extension
+
+        #if $singlePaired.sPaired == "single":
+            ln -s "${singlePaired.input_singles}" ./input_singles;
+        #elif $singlePaired.sPaired == "paired":
+            ln -s "${singlePaired.input_mate1}" ./input_mate1;
+            ln -s "${singlePaired.input_mate2}" ./input_mate2;
+        #else:
+            ln -s "${singlePaired.input_mate_pairs.forward}" ./input_mate1;
+            ln -s "${singlePaired.input_mate_pairs.reverse}" ./input_mate2;
+        #end if
+
+        perl $__tool_directory__/trim_galore
+
+        ## we only support fastqsanger
+        --phred33
+
+        #if $params.settingsType == "custom":
+
+            ## default 20
+            --quality $params.quality
+
+            ## default 1
+            --stringency $params.stringency
+
+            ## default 0.1
+            -e $params.error_rate
+
+            ## default 20
+            --length $params.min_length
+
+            #if $params.clip_R1:
+                --clip_R1 $params.clip_R1
+            #end if
+
+            #if $params.clip_R2:
+                --clip_R2 $params.clip_R2
+            #end if
+
+            #if $params.retain_unpaired.retain_unpaired_select == "retain_unpaired_output":
+                --retain_unpaired
+                --length_1 $params.retain_unpaired.length_1
+                --length_2 $params.retain_unpaired.length_2
+            #end if
+
+        #end if
+
+        ## RBBS specific options.
+        #if $rrbs.settingsType == "custom":
+            $rrbs.rrbs
+            $rrbs.non_directional
+        #end if
+
+        --output_dir ./
+        --suppress_warn
+
+        #if $params.settingsType == "custom" and not $params.report:
+            --no_report_file
+        #end if
+
+        #if $singlePaired.trimming.trimming_select == 'user':
+            ## default 'AGATCGGAAGAGC'
+            #if $singlePaired.trimming.adapter.strip() != '':
+               --adapter $singlePaired.trimming.adapter
+            #end if
+        #else:
+            $singlePaired.trimming.trimming_select
+        #end if
+
+
+        #if $singlePaired.three_prime_clip_R1:
+            --three_prime_clip_R1 $singlePaired.three_prime_clip_R1
+        #end if
+
+        #if $singlePaired.sPaired == "single":
+            ## input sequence
+            ./input_singles
+        #else:
+            --paired
+
+            $singlePaired.trim1
+
+            #if $singlePaired.trimming.trimming_select == 'user':
+                #if $singlePaired.trimming.adapter2 and $singlePaired.trimming.adapter2.strip() != '':
+                    --adapter2 $singlePaired.trimming.adapter2
+                #end if
+            #end if
+
+            #if $singlePaired.three_prime_clip_R2:
+                --three_prime_clip_R2 $singlePaired.three_prime_clip_R2
+            #end if
+
+            ## input sequences
+            ./input_mate1
+            ./input_mate2
+
+        #end if
+
+        ##  Trim Galore! run is finished. Move the report files to the proper place
+        #if $params.settingsType == "custom" and $params.report:
+            &&
+            cat ./*_trimming_report.txt > $report_file;
+        #end if
+
+]]>
+    </command>
+    <inputs>
+        <!-- Input Parameters -->
+        <conditional name="singlePaired">
+            <param name="sPaired" type="select" label="Is this library paired- or single-end?">
+                <option value="single">Single-end</option>
+                <option value="paired">Paired-end</option>
+                <option value="paired_collection">Paired Collection</option>
+            </param>
+            <when value="single">
+                <param name="input_singles" type="data" format="fastqsanger" label="Reads in FASTQ format" />
+                <expand macro="adapter_trimming"/>
+
+                <param name="three_prime_clip_R1" type="integer" value="" optional="True" label="Remove N bp from the 3' end">
+                    <help>Instructs Trim Galore! to remove N bp from the 3' end of read 1 after adapter/quality trimming has been performed.
+                        This may remove some unwanted bias from the 3' end that is not directly related to adapter sequence or basecall quality.
+                        (--three_prime_clip_R1)</help>
+                </param>
+            </when>
+            <when value="paired">
+                <param name="input_mate1" type="data" format="fastqsanger" label="Reads in FASTQ format" />
+                <param name="input_mate2" type="data" format="fastqsanger" label="Reads in FASTQ format" />
+                <expand macro="paired_adapter_trimming" />
+            </when>
+            <when value="paired_collection">
+                <param name="input_mate_pairs" format="fastqsanger" type="data_collection" collection_type="paired"
+                    label="Select a paired collection" help="See help section for an explanation of dataset collections"/>
+                <expand macro="paired_adapter_trimming" />
+            </when>
+        </conditional>
+
+        <conditional name="params">
+            <param name="settingsType" type="select" label="Trim Galore! advanced settings" help="You can use the default settings or set custom values for any of Trim Galore!'s parameters.">
+              <option value="default">Use defaults</option>
+              <option value="custom">Full parameter list</option>
+            </param>
+            <when value="default" />
+            <!-- Full/advanced params. -->
+            <when value="custom">
+                <param name="quality" type="integer" value="20" label="Trim low-quality ends from reads in addition to adapter removal"
+                    help="For more information please see below." />
+                <param name="stringency" type="integer" value="1" label="Overlap with adapter sequence required to trim a sequence" />
+                <param name="error_rate" type="float" value="0.1" label="Maximum allowed error rate" />
+                <param name="min_length" type="integer" value="20" label="Discard reads that became shorter than length INT" />
+
+                <param name="clip_R1" type="integer" optional="True" min="0" label="Instructs Trim Galore! to remove INT bp from the 5' end of read 1" />
+                <param name="clip_R2" type="integer" optional="True" min="0" label="Instructs Trim Galore! to remove INT bp from the 5' end of read 2" />
+
+                <param name="report" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Generate a report file" help="" />
+
+                <conditional name="retain_unpaired">
+                    <param name="retain_unpaired_select" type="select" label="specify if you would like to retain unpaired reads">
+                      <option value="no_output">Do not output unpaired reads</option>
+                      <option value="retain_unpaired_output">Output unpaired reads</option>
+                    </param>
+                    <when value="no_output" />
+                    <!-- Output params. -->
+                    <when value="retain_unpaired_output">
+                        <param name="length_1" type="integer" value="35" label="Unpaired single-end read length cutoff needed for read 1 to be written" />
+                        <param name="length_2" type="integer" value="35" label="Unpaired single-end read length cutoff needed for read 2 to be written" />
+                    </when>  <!-- output -->
+                </conditional>  <!-- retain_unpaired -->
+
+            </when>  <!-- full -->
+        </conditional>  <!-- params -->
+
+        <conditional name="rrbs">
+            <param name="settingsType" type="select" label="RRBS specific settings">
+              <option value="default">Use defaults (no RRBS)</option>
+              <option value="custom">Full parameter list</option>
+            </param>
+            <when value="default" />
+            <!-- Full/advanced params. -->
+            <when value="custom">
+                <param name="rrbs" type="boolean" truevalue="--rrbs" falsevalue="" checked="True"
+                    label="Specifies that the input file was an MspI digested RRBS sample" />
+                <param name="non_directional" type="boolean" truevalue="--non_directional" falsevalue="" checked="False"
+                    label="Selecting this option for non-directional RRBS libraries" />
+            </when>  <!-- full -->
+        </conditional>  <!-- params -->
+
+    </inputs>
+    <outputs>
+        <data format="fastqsanger" name="trimmed_reads_single" from_work_dir="input_singles_trimmed.fq" label="${tool.name} on ${on_string}: trimmed reads">
+            <filter>singlePaired['sPaired'] == "single"</filter>
+        </data>
+
+        <collection name="trimmed_reads_paired_collection" type="paired" label="${tool.name} on ${on_string}: paired reads">
+            <data name="forward" format="fastqsanger" from_work_dir="input_mate1_val_1.fq" />
+            <data name="reverse" format="fastqsanger" from_work_dir="input_mate2_val_2.fq" />
+            <filter>singlePaired['sPaired'] == "paired_collection"</filter>
+        </collection>
+
+        <collection name="trimmed_reads_unpaired_collection" type="paired" label="${tool.name} on ${on_string}: unpaired reads">
+            <data name="forward" format="fastqsanger" from_work_dir="input_mate1_unpaired_1.fq" />
+            <data name="reverse" format="fastqsanger" from_work_dir="input_mate2_unpaired_2.fq" />
+            <filter>params['settingsType'] == "custom"</filter>
+            <filter>params['retain_unpaired']['retain_unpaired_select'] == "retain_unpaired_output"</filter>
+            <filter>singlePaired['sPaired'] == "paired_collection"</filter>
+        </collection>
+
+        <data format="fastqsanger" name="trimmed_reads_pair1" from_work_dir="input_mate1_val_1.fq"
+            label="${tool.name} on ${on_string}: trimmed reads pair 1">
+            <filter>singlePaired['sPaired'] == "paired"</filter>
+        </data>
+
+        <data format="fastqsanger" name="trimmed_reads_pair2" from_work_dir="input_mate2_val_2.fq"
+            label="${tool.name} on ${on_string}: trimmed reads pair 2">
+            <filter>singlePaired['sPaired'] == "paired"</filter>
+        </data>
+
+        <data format="fastqsanger" name="unpaired_reads_1" from_work_dir="input_mate1_val_1.fq"
+            label="${tool.name} on ${on_string}: unpaired reads (1)">
+            <filter>params['settingsType'] == "custom"</filter>
+            <filter>params['retain_unpaired']['retain_unpaired_select'] == "retain_unpaired_output"</filter>
+            <filter>singlePaired['sPaired'] == "paired"</filter>
+        </data>
+
+        <data format="fastqsanger" name="unpaired_reads_2" from_work_dir="input_mate2_val_2.fq"
+            label="${tool.name} on ${on_string}: unpaired reads (2)">
+            <filter>params['settingsType'] == "custom"</filter>
+            <filter>params['retain_unpaired']['retain_unpaired_select'] == "retain_unpaired_output"</filter>
+            <filter>singlePaired['sPaired'] == "paired"</filter>
+        </data>
+        <data format="txt" name="report_file" label="${tool.name} on ${on_string}: report file">
+            <filter>params['settingsType'] == "custom"</filter>
+            <filter>params['report'] == True</filter>
+        </data>
+
+    </outputs>
+    <tests>
+        <test>
+            <param name="input_singles" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
+            <param name="sPaired" value="single" />
+            <param name="settingsType" value="custom" />
+            <param name="report" value="true" />
+            <output name="trimmed_reads_single" file="sanger_full_range_results1.fastqsanger" ftype="fastqsanger"/>
+            <output name="report_file" file="sanger_full_range_report_results1.txt" ftype="txt" lines_diff="2" />
+        </test>
+
+        <test>
+            <param name="input_singles" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
+            <param name="sPaired" value="single" />
+            <param name="trimming_select" value="--illumina" />
+            <output name="trimmed_reads_single" file="sanger_full_range_results2.fastqsanger" ftype="fastqsanger"/>
+        </test>
+
+        <test>
+            <param name="input_singles" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
+            <param name="sPaired" value="single" />
+            <param name="adapter" value="AAAGAGC" />
+            <output name="trimmed_reads_single" file="sanger_full_range_results3.fastqsanger" ftype="fastqsanger"/>
+        </test>
+
+        <test>
+            <param name="input_mate1" value="bwa-mem-fastq1.fq" ftype="fastqsanger" />
+            <param name="input_mate2" value="bwa-mem-fastq2.fq" ftype="fastqsanger" />
+            <param name="sPaired" value="paired" />
+            <param name="settingsType" value="custom" />
+            <param name="report" value="true" />
+            <output name="trimmed_reads_pair1" file="paired_example_pair1_results2.fastqsanger" ftype="fastqsanger"/>
+            <output name="trimmed_reads_pair2" file="paired_example_pair2_results2.fastqsanger" ftype="fastqsanger"/>
+            <output name="report_file" file="paired_example_results2.txt" ftype="txt" lines_diff="8" />
+        </test>
+
+        <test>
+            <param name="input_mate_pairs">
+                <collection type="paired">
+                    <element name="forward" value="bwa-mem-fastq1.fq" ftype="fastqsanger" />
+                    <element name="reverse" value="bwa-mem-fastq2.fq" ftype="fastqsanger" />
+                </collection>
+            </param>
+
+            <param name="sPaired" value="paired_collection" />
+            <param name="settingsType" value="custom" />
+            <param name="report" value="true" />
+            <param name="retain_unpaired_select" value="retain_unpaired_output" />
+
+            <output name="report_file" file="paired_collection_example_results3.txt" ftype="txt" lines_diff="8" />
+
+            <output_collection name="trimmed_reads_paired_collection" type="paired">
+                <element name="forward" file="paired_collection_example_pair1_results3.fastqsanger" ftype="fastqsanger"/>
+                <element name="reverse" file="paired_collection_example_pair2_results3.fastqsanger" ftype="fastqsanger"/>
+            </output_collection>
+
+            <output_collection name="trimmed_reads_unpaired_collection" type="paired">
+                <element name="forward" file="paired_collection_example_unpair1_results3.fastqsanger" ftype="fastqsanger"/>
+                <element name="reverse" file="paired_collection_example_unpair2_results3.fastqsanger" ftype="fastqsanger"/>
+            </output_collection>
+
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+**What it does**
+
+`Trim Galore!`_ is a wrapper script to automate quality and adapter trimming as well as quality control, with some added functionality to remove biased methylation positions for RRBS sequence files (for directional, non-directional (or paired-end) sequencing). It's main features are:
+
+ * For adapter trimming, Trim Galore! uses the first 13 bp of Illumina standard adapters ('AGATCGGAAGAGC') by default (suitable for both ends of paired-end libraries), but accepts other adapter sequence, too
+ * For MspI-digested RRBS libraries, Trim Galore! performs quality and adapter trimming in two subsequent steps. This allows it to remove 2 additional bases that contain a cytosine which was artificially introduced in the end-repair step during the library preparation
+ * For any kind of FASTQ file other than MspI-digested RRBS, Trim Galore! can perform single-pass adapter and quality trimming
+ * The Phred quality of basecalls and the stringency for adapter removal can be specified individually
+ * Trim Galore! can remove sequences if they become too short during the trimming process. For paired-end files Trim Galore! removes entire sequence pairs if one (or both) of the two reads became shorter than the set length cutoff. Reads of a read-pair that are longer than a given threshold but for which the partner read has become too short can optionally be written out to single-end files. This ensures that the information of a read pair is not lost entirely if only one read is of good quality
+ * Trim Galore! can trim paired-end files by 1 additional bp from the 3' end of all reads to avoid problems with invalid alignments with Bowtie 1
+
+.. _Trim Galore!: http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/
+
+It is developed by Felix Krueger at the Babraham Institute.
+]]>
+    </help>
+    <citations></citations>
+</tool>