Mercurial > repos > bgruening > trim_galore
changeset 8:f1e71aeaa923 draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit d48f42b1c267c8ebfc50161ea764baed8ee66701-dirty
| author | bgruening |
|---|---|
| date | Fri, 18 Mar 2016 07:56:01 -0400 |
| parents | 8352713cf939 |
| children | 1bfc7254232e |
| files | trim_galore.xml |
| diffstat | 1 files changed, 65 insertions(+), 13 deletions(-) [+] |
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--- a/trim_galore.xml Mon Jan 25 04:44:33 2016 -0500 +++ b/trim_galore.xml Fri Mar 18 07:56:01 2016 -0400 @@ -1,4 +1,4 @@ -<tool id="trim_galore" name="Trim Galore!" version="0.4.1"> +<tool id="trim_galore" name="Trim Galore!" version="0.4.2"> <!-- Wrapper compatible with Trim Galore! version 0.4 --> <description>adaptive quality and adapter trimmer</description> <macros> @@ -44,9 +44,13 @@ </macro> </macros> <requirements> + <!-- conda dependency --> + <requirement type="package" version="1.8.3">cutadapt</requirement> <requirement type="package" version="1.8">cutadapt</requirement> </requirements> - <version_command interpreter="perl">trim_galore --version</version_command> + <version_command> + perl $__tool_directory__/trim_galore --version + </version_command> <command> <![CDATA[ @@ -56,13 +60,27 @@ ## We work around this by linking every file to cwd without file extension #if $singlePaired.sPaired == "single": - ln -s "${singlePaired.input_singles}" ./input_singles; + #if str($singlePaired.input_singles).endswith(".gz"): + ln -s "${singlePaired.input_singles}" ./input_singles.gz; + #else + ln -s "${singlePaired.input_singles}" ./input_singles; + #end if #elif $singlePaired.sPaired == "paired": - ln -s "${singlePaired.input_mate1}" ./input_mate1; - ln -s "${singlePaired.input_mate2}" ./input_mate2; + #if str($singlePaired.input_mate1).endswith(".gz"): + ln -s "${singlePaired.input_mate1}" ./input_mate1.gz; + ln -s "${singlePaired.input_mate2}" ./input_mate2.gz; + #else + ln -s "${singlePaired.input_mate1}" ./input_mate1; + ln -s "${singlePaired.input_mate2}" ./input_mate2; + #end if #else: - ln -s "${singlePaired.input_mate_pairs.forward}" ./input_mate1; - ln -s "${singlePaired.input_mate_pairs.reverse}" ./input_mate2; + #if str($singlePaired.input_mate_pairs.forward).endswith(".gz"): + ln -s "${singlePaired.input_mate_pairs.forward}" ./input_mate1.gz; + ln -s "${singlePaired.input_mate_pairs.reverse}" ./input_mate2.gz; + #else + ln -s "${singlePaired.input_mate_pairs.forward}" ./input_mate1; + ln -s "${singlePaired.input_mate_pairs.reverse}" ./input_mate2; + #end if #end if perl $__tool_directory__/trim_galore @@ -129,7 +147,12 @@ #if $singlePaired.sPaired == "single": ## input sequence - ./input_singles + #if str($singlePaired.input_singles).endswith(".gz"): + ./input_singles.gz + --dont_gzip + #else + ./input_singles + #end if #else: --paired @@ -146,11 +169,40 @@ #end if ## input sequences - ./input_mate1 - ./input_mate2 + #if $singlePaired.sPaired == "paired": + #if str($singlePaired.input_mate1).endswith(".gz"): + ./input_mate1.gz + ./input_mate2.gz + --dont_gzip + #else + ./input_mate1 + ./input_mate2 + #end if + #else: + #if str($singlePaired.input_mate_pairs.forward).endswith(".gz"): + ./input_mate1.gz + ./input_mate2.gz + --dont_gzip + #else + ./input_mate1 + ./input_mate2 + #end if + #end if #end if + ## Trim Galore is finished, rename the output if compressed + && + if [ -f input_singles.gz_trimmed.fq ] ; then mv input_singles.gz_trimmed.fq input_singles_trimmed.fq ; fi + && + if [ -f input_mate1.gz_val_1.fq ] ; then mv input_mate1.gz_val_1.fq input_mate1_val_1.fq ; fi + && + if [ -f input_mate2.gz_val_2.fq ] ; then mv input_mate2.gz_val_2.fq input_mate2_val_2.fq ; fi + && + if [ -f input_mate1.gz_unpaired_1.fq ] ; then mv input_mate1.gz_unpaired_1.fq input_mate1_unpaired_1.fq ; fi + && + if [ -f input_mate2.gz_unpaired_2.fq ] ; then mv input_mate2.gz_unpaired_2.fq input_mate2_unpaired_2.fq ; fi + ## Trim Galore! run is finished. Move the report files to the proper place #if $params.settingsType == "custom" and $params.report: && @@ -295,7 +347,7 @@ <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" /> + <output name="report_file" file="sanger_full_range_report_results1.txt" ftype="txt" lines_diff="8" /> </test> <test> @@ -320,7 +372,7 @@ <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" /> + <output name="report_file" file="paired_example_results2.txt" ftype="txt" lines_diff="24" /> </test> <test> @@ -336,7 +388,7 @@ <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 name="report_file" file="paired_collection_example_results3.txt" ftype="txt" lines_diff="24" /> <output_collection name="trimmed_reads_paired_collection" type="paired"> <element name="forward" file="paired_collection_example_pair1_results3.fastqsanger" ftype="fastqsanger"/>