Mercurial > repos > dfornika > confindr
changeset 0:d43117b98027 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/confindr/ commit 9e41ac63171c3e3a6fd2b4d018d0c60c9f1fbae1"
author | dfornika |
---|---|
date | Fri, 31 Jan 2020 18:28:41 +0000 |
parents | |
children | 627b2e75b1ad |
files | confindr.xml macros.xml |
diffstat | 2 files changed, 114 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/confindr.xml Fri Jan 31 18:28:41 2020 +0000 @@ -0,0 +1,80 @@ +<tool id="confindr" name="ConFindr" version="@VERSION@+galaxy0"> + <description> + Intra-species bacterial contamination detection + </description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <expand macro="version_command" /> + + <command detect_errors="exit_code"><![CDATA[ + #if str( $reads_input.reads_input_selector ) == "paired" + ln -s '$reads_input.reads_1' 'input/reads_R1.fastq.gz' && + ln -s '$reads_input.reads_2' 'input/reads_R2.fastq.gz' && + #end if + #if str( $reads_input.reads_input_selector ) == "paired_collection" + ln -s '$reads_input.reads.forward' 'input/reads_R1.fastq.gz' && + ln -s '$reads_input.reads.reverse' 'input/reads_R2.fastq.gz' && + #end if + + confindr.py + --input_directory input \ + --output_name output \ + + ]]></command> + + <inputs> + <conditional name="reads_input"> + <param name="reads_input_selector" type="select" label="Paired-end reads or paired collection" help="Select between paired and paired collection"> + <option value="paired">Paired</option> + <option value="paired_collection">Paired Collection</option> + </param> + <when value="paired"> + <param name="reads_1" type="data" format="@INTYPES@" label="Select first set of reads" help="Specify dataset with forward reads"/> + <param name="reads_2" type="data" format="@INTYPES@" label="Select second set of reads" help="Specify dataset with reverse reads"/> + </when> + <when value="paired_collection"> + <param name="reads" format="@INTYPES@" type="data_collection" collection_type="paired" label="Select a paired collection" help="See help section for an explanation of dataset collections"/> + </when> + </conditional> + </inputs> + + <outputs> + <data name="report" format="tabular" from_work_dir="output/confindr_report.csv" label="${tool.name} on ${on_string} report file" /> + </outputs> + + <tests> + + + </tests> + + <help><![CDATA[ +**What it does** + + + +**Output** + +ConFindr will produce a tab-seperated output file with the following outputs: + ++---------------+------------------------------------------------+ +| Column | Description | ++===============+================================================+ +| | | ++---------------+------------------------------------------------+ +| | | ++---------------+------------------------------------------------+ +| | | ++---------------+------------------------------------------------+ + + +**Example Output** + +:: + + + ]]></help> + + <expand macro="citations"/> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Fri Jan 31 18:28:41 2020 +0000 @@ -0,0 +1,34 @@ +<macros> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@VERSION@">confindr</requirement> + <yield /> + </requirements> + </xml> + + <xml name="version_command"> + <version_command><![CDATA[confindr.py --version]]></version_command> + </xml> + + <token name="@VERSION@">0.7.2</token> + + <token name="@INTYPES"> + fastq.gz,fastqsanger.gz + </token> + + <xml name="citations"> + <citations> + <citation type="bibtex"> + @article{low2019confindr, + title={ConFindr: rapid detection of intraspecies and cross-species contamination in bacterial whole-genome sequence data}, + author={Low, Andrew J and Koziol, Adam G and Manninger, Paul A and Blais, Burton and Carrillo, Catherine D}, + journal={PeerJ}, + volume={7}, + pages={e6995}, + year={2019}, + publisher={PeerJ Inc.} + } + </citation> + </citations> + </xml> +</macros>