Mercurial > repos > mingchen0919 > statonlab_hmmscan

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author mingchen0919
date Sun, 16 Sep 2018 10:59:01 -0400
parents 6ec32fcdba69
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1 <tool id="statonlab_hmmscan" name="aurora_statonlab_hmmscan" version="1.0.0">
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2 <description>Query protein sequences against Pfam database&#xD;
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3 </description>
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4 <requirements>
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5 <requirement type="package" version="1.15.0.6-0">pandoc</requirement>
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6 <requirement type="package" version="1.20.0">r-getopt</requirement>
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7 <requirement type="package" version="3.2.1">hmmer</requirement>
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8 <requirement type="package" version="1.6">r-rmarkdown</requirement>
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9 <requirement type="package" version="0.8.1">seqkit</requirement>
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10 <requirement type="package" version="1.1.1">r-tidyverse</requirement>
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11 </requirements>
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12 <command><![CDATA[ ######### each aurora tool generates a html file and have an files path directory associated with it.
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13 mkdir -p $report.files_path &&
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14
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15 ######### three important paths:
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16 ######### 1. path to tool installation directory
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17 ######### 2. path to report html
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18 ######### 3. path to files_path directory associated with the report output.
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19 export TOOL_INSTALL_DIR='${__tool_directory__}' &&
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20 export REPORT='$report' &&
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21 export REPORT_FILES_PATH='$report.files_path' &&
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22
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23 ############ create a hidden file to store r markdown rendering log
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24 touch $report.files_path/r_rendering.log.txt &&
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25
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26 ############ finally run the render.R script
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27 Rscript '${__tool_directory__}/rmarkdown_report_render.R'
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28
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29 -o $report
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30 -d $report.files_path
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31 -g $significant_genes
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32 -u $protein_sequences_url
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33
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34 -E $evalue_threshold
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35 -T $score_threshold
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36 -e $domE
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37 -t $domT
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38 -b $best_hit
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39 -1 $pfam_tbl_out
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40 ]]></command>
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41 <inputs>
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42 <param type="data" name="significant_genes" label="Significant Genes"
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43 help="A significant genes file from the &lt;code&gt;aurora_deseq2&lt;/code&gt; tool." optional="False"
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44 format="txt,csv" multiple="False"/>
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45 <param type="text" name="protein_sequences_url" label="URL to a protein sequences file" optional="False"/>
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46 <param type="text" name="evalue_threshold" argument="-E" label="Evalue threshold" optional="True"
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47 help="report models &lt;= this E-value threshold in output [10.0] (x&gt;0)" optional="False"
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48 value="10"/>
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49 <param type="text" name="score_threshold" argument="-T" label="Score threshold" optional="True"
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50 help="report models &gt;= this score threshold in output" optional="False"/>
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51 <param type="text" name="domE" argument="--domE" label="domains E-value threshold" optional="True"
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52 help="report domains &lt;= this E-value threshold in output [10.0] (x&gt;0)" optional="False"
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53 value="10"/>
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54 <param type="text" name="domT" argument="--domT" label="domains score threshold" optional="True"
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55 help="report domains &gt;= this score cutoff in output" optional="False"/>
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56 <param type="boolean" name="best_hit" label="Best Hit" help="Only return best hit for each query sequence"
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57 optional="False" truevalue="NO_ARGUMENT_YES" falsevalue="NO_ARGUMENT_NO"/>
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58 </inputs>
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59 <outputs>
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60 <data format="html" name="report" label="${tool.name} report on ${on_string}"/>
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61 <data name="pfam_tbl_out" format="csv" label="${tool.name} pfam.domtblout on ${on_string}" hidden="false"/>
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62 </outputs>
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63 <citations>
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64 <citation type="bibtex"><![CDATA[
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65 @article{allaire2016rmarkdown,
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66 title={rmarkdown: Dynamic Documents for R, 2016},
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67 author={Allaire, J and Cheng, Joe and Xie, Yihui and McPherson, Jonathan and Chang, Winston and Allen, Jeff
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68 and Wickham, Hadley and Atkins, Aron and Hyndman, Rob},
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69 journal={R package version 0.9},
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70 volume={6},
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71 year={2016}
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72 }
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73 ]]></citation>
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74 <citation type="bibtex"><![CDATA[
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75 @book{xie2015dynamic,
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76 title={Dynamic Documents with R and knitr},
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77 author={Xie, Yihui},
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78 volume={29},
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79 year={2015},
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80 publisher={CRC Press}
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81 }
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82 ]]></citation>
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83 <citation type="bibtex"><![CDATA[
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84 @online{jstree,
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85 author={Bozhanov, Ivan},
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86 year = 2018,
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87 url = {https://www.jstree.com/}
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88 }
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89 ]]></citation>
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90 <citation type="bibtex"><![CDATA[@article{eddy1992hmmer,
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91 title={HMMER user’s guide},
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92 author={Eddy, Sean},
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93 journal={Department of Genetics, Washington University School of Medicine},
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94 volume={2},
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95 number={1},
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96 year={1992}
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97 }]]></citation>
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98 </citations>
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99 </tool>