Mercurial > repos > iuc > presto_pairseq
changeset 3:49e7407445c3 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit d52e3c9c53dd358e14e65a3a083e7d5c102f8697"
| author | iuc |
|---|---|
| date | Sat, 25 Sep 2021 18:34:52 +0000 |
| parents | 7bdff30820bf |
| children | eed465eb14a3 |
| files | presto_macros.xml presto_pairseq.xml |
| diffstat | 2 files changed, 43 insertions(+), 12 deletions(-) [+] |
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--- a/presto_macros.xml Fri Jul 02 15:31:14 2021 +0000 +++ b/presto_macros.xml Sat Sep 25 18:34:52 2021 +0000 @@ -5,9 +5,14 @@ <yield /> </citations> </xml> - + <xml name="bio_tools"> + <xrefs> + <xref type="bio.tools">presto</xref> + </xrefs> + </xml> <token name="@TOOL_VERSION@">0.6.2</token> - + <token name="@VERSION_SUFFIX@">0</token> + <token name="@PROFILE@">20.05</token> <xml name="requirements"> <requirements> <requirement type="package" version="@TOOL_VERSION@">presto</requirement> @@ -42,7 +47,7 @@ <token name="@HELP_NOTE@"><![CDATA[ -==== +=== **Note about limitations of pRESTO tools within Galaxy:**
--- a/presto_pairseq.xml Fri Jul 02 15:31:14 2021 +0000 +++ b/presto_pairseq.xml Sat Sep 25 18:34:52 2021 +0000 @@ -1,12 +1,12 @@ -<tool id="presto_pairseq" name="pRESTO PairSeq" version="@TOOL_VERSION@"> +<tool id="presto_pairseq" name="pRESTO PairSeq" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> <description>Sorts and matches sequence records with matching coordinates across files</description> - + <expand macro="bio_tools"/> <macros> <import>presto_macros.xml</import> - </macros> - - <expand macro="requirements"/> - + </macros> + + <expand macro="requirements"/> + <version_command>PairSeq.py --version</version_command> <command detect_errors="exit_code"><![CDATA[ ln -s '$r1_in' r1.fastq && @@ -21,6 +21,7 @@ #if $r2_annotations --2f $r2_annotations #end if + $failed --outdir=. --outname=tmp ]]></command> @@ -34,14 +35,21 @@ <expand macro="text-regex-validator"/> </param> <expand macro="presto-coord-param"/> + <param argument="--failed" type="boolean" checked="false" truevalue="--failed" falsevalue="" label="Failed reads fastq output" /> </inputs> <outputs> <data name="r1_out" format="fastq" from_work_dir="tmp-1_pair-pass.fastq"/> <data name="r2_out" format="fastq" from_work_dir="tmp-2_pair-pass.fastq"/> + <!-- only give these 2 outputs if input failed_fastq=True--> + <data name="r1_fail_out" format="fastq" from_work_dir="tmp-1_pair-fail.fastq"> + <filter>failed</filter> + </data> + <data name="r2_fail_out" format="fastq" from_work_dir="tmp-2_pair-fail.fastq"> + <filter>failed</filter> + </data> </outputs> - <tests> - <test> + <test expect_num_outputs="2"> <param name="r1_in" value="presto_pairseq_test1_r1_in.fastq"/> <param name="r2_in" value="presto_pairseq_test1_r2_in.fastq"/> <param name="r2_annotations" value="BARCODE"/> @@ -49,8 +57,26 @@ <output name="r1_out" file="presto_pairseq_test1_r1_out.fastq" sort="true"/> <output name="r2_out" file="presto_pairseq_test1_r2_out.fastq" sort="true"/> </test> + <test expect_num_outputs="4"> + <param name="r1_in" value="presto_pairseq_test1_r1_in.fastq"/> + <param name="r2_in" value="presto_pairseq_test1_r2_in.fastq"/> + <param name="r2_annotations" value="BARCODE"/> + <param name="coord" value="illumina"/> + <param name="failed" value="true"/> + <output name="r1_out" file="presto_pairseq_test1_r1_out.fastq" sort="true"/> + <output name="r2_out" file="presto_pairseq_test1_r2_out.fastq" sort="true"/> + <output name="r1_fail_out"> + <assert_contents> + <has_text text="@"/> + </assert_contents> + </output> + <output name="r2_fail_out"> + <assert_contents> + <has_text text="@"/> + </assert_contents> + </output> + </test> </tests> - <help><![CDATA[ Sorts and matches sequence records with matching coordinates across files.