Mercurial > repos > iuc > presto_pairseq
changeset 4:1df9f64cddd5 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit d52e3c9c53dd358e14e65a3a083e7d5c102f8697"
| author | iuc |
|---|---|
| date | Sat, 25 Sep 2021 18:27:45 +0000 |
| parents | a4994292ab59 |
| children | 002cc03c4217 |
| files | presto_macros.xml presto_macros.xml.orig presto_pairseq.xml |
| diffstat | 3 files changed, 37 insertions(+), 75 deletions(-) [+] |
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--- a/presto_macros.xml Wed Sep 01 08:14:30 2021 +0000 +++ b/presto_macros.xml Sat Sep 25 18:27:45 2021 +0000 @@ -11,7 +11,8 @@ </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> @@ -46,7 +47,7 @@ <token name="@HELP_NOTE@"><![CDATA[ -==== +=== **Note about limitations of pRESTO tools within Galaxy:**
--- a/presto_macros.xml.orig Wed Sep 01 08:14:30 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,65 +0,0 @@ -<macros> - <xml name="citations"> - <citations> - <citation type="doi">10.1093/bioinformatics/btu138</citation> - <yield /> - </citations> - </xml> -<<<<<<< HEAD - - <token name="@TOOL_VERSION@">0.6.2</token> - -======= - <xml name="bio_tools"> - <xrefs> - <xref type='bio.tools'>presto</xref> - </xrefs> - </xml> ->>>>>>> 7abad681f (add tools up until P) - <xml name="requirements"> - <requirements> - <requirement type="package" version="@TOOL_VERSION@">presto</requirement> - </requirements> - </xml> - - <xml name="presto-coord-param"> - <param argument="--coord" type="select" value="presto" label="Coordinate" help="The format of the sequence identifier which defines shared coordinate information across mate pairs."> - <option value="illumina">Illumina</option> - <option value="solexa">Solexa</option> - <option value="sra">SRA</option> - <option value="454">454</option> - <option value="presto">pRESTO</option> - </param> - </xml> - - <xml name="presto-log-param"> - <param name="capture_log" type="boolean" value="false" label="Generate Detailed Log" help="Generate detailed log information that can be summarized with ParseLog."/> - </xml> - - <xml name="presto-log-output"> - <data name="log_out" format="txt" label="Log from ${tool.name} on ${on_string}"> - <filter>capture_log</filter> - </data> - </xml> - - <xml name="text-regex-validator"> - <validator type="regex" message="Value may include alphanumeric characters, underscores and spaces.">[A-Za-z0-9_ ]+</validator> - </xml> - - <token name="@PRESTO_URL_BASE@">https://presto.readthedocs.io</token> - - <token name="@HELP_NOTE@"><![CDATA[ - -==== - -**Note about limitations of pRESTO tools within Galaxy:** - -pRESTO tools in galaxy have the following limitations vs. when run at the command line: - -* Inputs must be FASTQ format and cannot be FASTA format. -* Multiple inputs files are not supported per argument (e.g. ``-1``, ``-2`` or ``-s``), i.e. - - Steps that take a pair of fastq inputs can only take two files, not two sets of files - - Steps that take a single set of fastq inputs can only take a single file -* The ``--outdir`` and ``--outname`` options are not supported; output files are named directly - ]]></token> -</macros>
--- a/presto_pairseq.xml Wed Sep 01 08:14:30 2021 +0000 +++ b/presto_pairseq.xml Sat Sep 25 18:27:45 2021 +0000 @@ -1,12 +1,12 @@ -<tool id="presto_pairseq" name="pRESTO PairSeq" version="@TOOL_VERSION@"> +<tool id="presto_pairseq" name="pRESTO PairSeq" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> <description>Sorts and matches sequence records with matching coordinates across files</description> <expand macro="bio_tools"/> <macros> <import>presto_macros.xml</import> - </macros> - - <expand macro="requirements"/> - + </macros> + + <expand macro="requirements"/> + <version_command>PairSeq.py --version</version_command> <command detect_errors="exit_code"><![CDATA[ ln -s '$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.