trim_galore: trim_galore.xml comparison

comparison trim_galore.xml @ 11:80cd83b11214 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 78bee2b2efd36fe9399ce574159fc007cb6bdfbf

author	bgruening
date	Mon, 24 Apr 2017 14:30:07 -0400
parents	b4e39d993fc8
children	1bf4789584dc

comparison

equal deleted inserted replaced

-:b4e39d993fc8
+:80cd83b11214
-<tool id="trim_galore" name="Trim Galore!" version="0.4.3" profile="17.01">
+<tool id="trim_galore" name="Trim Galore!" version="0.4.3.0" profile="17.01">
-<!-- Wrapper compatible with Trim Galore! version 0.4 -->
+<!-- Wrapper compatible with Trim Galore! version 0.4.3 -->
 <description>Quality and adapter trimmer of reads</description>
 <macros>
 <macro name="adapter_trimming">
 <conditional name="trimming">
 <param name="trimming_select" type="select" label="Adapter sequence to be trimmed">
 <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]*$</validator>
 </param>
 </expand>
 the 3' end that is not directly related to adapter sequence or basecall quality.</help>
 </param>
 </macro>
 </macros>
 <requirements>
-<!-- conda dependency -->
+<requirement type="package" version="0.4.3">trim-galore</requirement>
-<requirement type="package" version="1.8.3">cutadapt</requirement>
-<requirement type="package" version="1.8">cutadapt</requirement>
 </requirements>
 <version_command>
-perl '$__tool_directory__/trim_galore' --version
+trim_galore --version
 </version_command>
-<command>
+<command><![CDATA[
-<![CDATA[
 #set compressed = 'no'
 #if $singlePaired.sPaired == "single":
 #if $singlePaired.input_singles.is_of_type("fastq.gz"):
 #set read1 = 'input_1.fastq.gz'
 #set compressed = 'gz'
 #set read2 = 'input_2.fastq'
 #end if
 ln -s '${singlePaired.input_mate_pairs.reverse}' ${read2} &&
 #end if
-perl '$__tool_directory__/trim_galore'
+trim_galore
 ## we only support fastqsanger
 --phred33
 #if $params.settingsType == "custom":
 #end if
 #if $singlePaired.trimming.trimming_select == 'user':
 ## default 'AGATCGGAAGAGC'
 #if $singlePaired.trimming.adapter.strip() != '':
---adapter $singlePaired.trimming.adapter
+--adapter '$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
 $singlePaired.trim1
 #if $singlePaired.trimming.trimming_select == 'user':
 #if $singlePaired.trimming.adapter2 and $singlePaired.trimming.adapter2.strip() != '':
---adapter2 $singlePaired.trimming.adapter2
+--adapter2 '$singlePaired.trimming.adapter2'
 #end if
 #end if
 #if $singlePaired.three_prime_clip_R2:
 --three_prime_clip_R2 $singlePaired.three_prime_clip_R2
 if [ -f input_2_unpaired_2.fq.gz ] ; then mv input_2_unpaired_2.fq.gz input_2_unpaired_2.fq ; fi
 ##  Trim Galore! run is finished. Move the report files to the proper place
 #if $params.settingsType == "custom" and $params.report:
 &&
-cat ./*_trimming_report.txt > $report_file;
+cat ./*_trimming_report.txt > '$report_file'
 #end if
+]]></command>
-]]>
-</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>
 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="Screen quality-trimmed sequences for 'CAA' or 'CGA' at the start of the read and, if found, removes the first two basepairs" />
 </when>  <!-- full -->
 </conditional>  <!-- params -->
 </inputs>
 <outputs>
 <data format_source="input_singles" name="trimmed_reads_single" from_work_dir="input_1_trimmed.fq" label="${tool.name} on ${on_string}: trimmed reads">
 <filter>singlePaired['sPaired'] == "single"</filter>
 </data>
 </data>
 <data format="txt" name="report_file" label="${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" />
 <element name="forward" file="paired_collection_example_unpair1_results3.fastq.gz" ftype="fastqsanger.gz" compare="sim_size" delta="0"/>
 <element name="reverse" file="paired_collection_example_unpair2_results3.fastq.gz" ftype="fastqsanger.gz" compare="sim_size" delta="0"/>
 </output_collection>
 </test>
 </tests>
-<help>
+<help><![CDATA[
-<![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
 **Main Settings**
 * **Adapter sequence to be trimmed**
 * **Automatic detection**
 | Adapter sequence to be trimmed. Trim Galore will try to auto-detect whether the Illumina universal, Nextera transposase or Illumina small RNA adapter sequence was used.
 * **Illumina universal**
 | Adapter sequence to be trimmed is the first 13bp of the Illumina universal adapter 'AGATCGGAAGAGC' instead of the default auto-detection of adapter sequence.
 |
 |   R1 --------------------------->
 |   R2 <---------------------------
 |
 | or this:
 |
 |   R1 ----------------------->
 |   R2 <-----------------
 |
 | as invalid (whenever a start/end coordinate is contained within the other read).
 |
 * **Screen quality-trimmed sequences for 'CAA' or 'CGA' at the start of the read and, if found, removes the first two basepairs**
 | Selecting this option for non-directional RRBS libraries will screen quality-trimmed sequences for 'CAA' or 'CGA' at the start of the read and, if found, removes the first two basepairs. Like with the option '--rrbs' this avoids using cytosine positions that were filled-in during the end-repair step. '--non_directional' requires '--rrbs' to be specified as well.
 |
-| *option --non_directional*]]>
+| *option --non_directional*
-</help>
+]]></help>
 <citations></citations>
 </tool>

Mercurial > repos > bgruening > trim_galore

comparison trim_galore.xml @ 11:80cd83b11214 draft