Mercurial > repos > mingchen0919 > statonlab_hmmscan
diff rmarkdown_report.xml @ 9:a7256d37a33b draft
planemo upload commit 690c4bb06a00f1a035c746c3d283a3026ecf6319-dirty
| author | mingchen0919 |
|---|---|
| date | Sun, 16 Sep 2018 10:04:25 -0400 |
| parents | e3ff9e38c40c |
| children | 6ec32fcdba69 |
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--- a/rmarkdown_report.xml Fri Sep 14 15:55:01 2018 -0400 +++ b/rmarkdown_report.xml Sun Sep 16 10:04:25 2018 -0400 @@ -1,9 +1,15 @@ <tool id="statonlab_hmmscan" name="aurora_statonlab_hmmscan" version="1.0.0"> - <description>Query protein sequences against Pfam database
 + <description>Query protein sequences against Pfam database
 </description> - <requirements> - <requirement type="package" version="1.15.0.6-0">pandoc</requirement><requirement type="package" version="1.20.0">r-getopt</requirement><requirement type="package" version="3.2.1">hmmer</requirement><requirement type="package" version="1.6">r-rmarkdown</requirement><requirement type="package" version="0.8.1">seqkit</requirement><requirement type="package" version="1.0.0">r-tidyverse</requirement></requirements> - <command><![CDATA[ ######### each aurora tool generates a html file and have an files path directory associated with it. + <requirements> + <requirement type="package" version="1.15.0.6-0">pandoc</requirement> + <requirement type="package" version="1.20.0">r-getopt</requirement> + <requirement type="package" version="3.2.1">hmmer</requirement> + <requirement type="package" version="1.6">r-rmarkdown</requirement> + <requirement type="package" version="0.8.1">seqkit</requirement> + <requirement type="package" version="1.0.0">r-tidyverse</requirement> + </requirements> + <command><![CDATA[ ######### each aurora tool generates a html file and have an files path directory associated with it. mkdir -p $report.files_path && ######### three important paths: @@ -32,11 +38,29 @@ -b $best_hit -1 $pfam_tbl_out ]]></command> - <inputs> - <param type="data" name="significant_genes" label="Significant Genes" help="A significant genes file from the <code>aurora_deseq2</code> tool." optional="False" format="txt,csv" multiple="False"/><param type="text" name="protein_sequences_url" label="URL to a protein sequences file" optional="False"/><param type="text" name="evalue_threshold" argument="-E" label="Evalue threshold" help="report models <= this E-value threshold in output [10.0] (x>0)" optional="False" value="10"/><param type="text" name="score_threshold" argument="-T" label="Score threshold" help="report models >= this score threshold in output" optional="False"/><param type="text" name="domE" argument="--domE" label="domains E-value threshold" help="report domains <= this E-value threshold in output [10.0] (x>0)" optional="False" value="10"/><param type="boolean" name="best_hit" label="Best Hit" help="Only return best hit for each query sequence" optional="False" truevalue="NO_ARGUMENT_YES" falsevalue="NO_ARGUMENT_NO"/><param type="text" name="domT" argument="--domT" label="domains score threshold" help="report domains >= this score cutoff in output" optional="False"/></inputs> - <outputs> - <data format="html" name="report" label="${tool.name} report on ${on_string}"/><data name="pfam_tbl_out" format="txt" label="${tool.name} pfam.domtblout on ${on_string}" hidden="false"/></outputs> - <citations> + <inputs> + <param type="data" name="significant_genes" label="Significant Genes" + help="A significant genes file from the <code>aurora_deseq2</code> tool." optional="False" + format="txt,csv" multiple="False"/> + <param type="text" name="protein_sequences_url" label="URL to a protein sequences file" optional="False"/> + <param type="text" name="evalue_threshold" argument="-E" label="Evalue threshold" + help="report models <= this E-value threshold in output [10.0] (x>0)" optional="False" + value="10"/> + <param type="text" name="score_threshold" argument="-T" label="Score threshold" + help="report models >= this score threshold in output" optional="False"/> + <param type="text" name="domE" argument="--domE" label="domains E-value threshold" + help="report domains <= this E-value threshold in output [10.0] (x>0)" optional="False" + value="10"/> + <param type="text" name="domT" argument="--domT" label="domains score threshold" + help="report domains >= this score cutoff in output" optional="False"/> + <param type="boolean" name="best_hit" label="Best Hit" help="Only return best hit for each query sequence" + optional="False" truevalue="NO_ARGUMENT_YES" falsevalue="NO_ARGUMENT_NO"/> + </inputs> + <outputs> + <data format="html" name="report" label="${tool.name} report on ${on_string}"/> + <data name="pfam_tbl_out" format="csv" label="${tool.name} pfam.domtblout on ${on_string}" hidden="false"/> + </outputs> + <citations> <citation type="bibtex"><![CDATA[ @article{allaire2016rmarkdown, title={rmarkdown: Dynamic Documents for R, 2016}, @@ -46,7 +70,8 @@ volume={6}, year={2016} } - ]]></citation><citation type="bibtex"><![CDATA[ + ]]></citation> + <citation type="bibtex"><![CDATA[ @book{xie2015dynamic, title={Dynamic Documents with R and knitr}, author={Xie, Yihui}, @@ -54,18 +79,21 @@ year={2015}, publisher={CRC Press} } - ]]></citation><citation type="bibtex"><![CDATA[ + ]]></citation> + <citation type="bibtex"><![CDATA[ @online{jstree, author={Bozhanov, Ivan}, year = 2018, url = {https://www.jstree.com/} } - ]]></citation><citation type="bibtex"><![CDATA[@article{eddy1992hmmer, - title={HMMER user’s guide}, - author={Eddy, Sean}, - journal={Department of Genetics, Washington University School of Medicine}, - volume={2}, - number={1}, - year={1992} -}]]></citation></citations> + ]]></citation> + <citation type="bibtex"><![CDATA[@article{eddy1992hmmer, + title={HMMER user’s guide}, + author={Eddy, Sean}, + journal={Department of Genetics, Washington University School of Medicine}, + volume={2}, + number={1}, + year={1992} +}]]></citation> + </citations> </tool>