Mercurial > repos > mingchen0919 > rmarkdown_bdss_client

annotate bdss_client_sra.xml @ 26:fb8f1d1ceeae draft

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planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit b212086a85c4d1e62e0d0c0e77b6f3fcabea04ef
author mingchen0919
date Sun, 15 Oct 2017 23:03:44 -0400
parents a1c0ebd05f2f
children 6efe73e1f06d
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1 <tool id="rmarkdown_bdss_client_sra" name="BDSS client SRA" version="1.0.3">
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2 <requirements>
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3 <requirement type="package" version="1.15.0.6-0">pandoc</requirement>
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4 <requirement type="package" version="3.3.2">r-base</requirement>
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5 <requirement type="package" version="1.20.0">r-getopt</requirement>
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6 <requirement type="package" version="1.2">r-rmarkdown</requirement>
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7 <requirement type="package" version="0.3.5">r-htmltools</requirement>
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8 <requirement type="package" version="0.5.0">r-dplyr</requirement>
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9 <requirement type="package" version="0.5.4">parallel-fastq-dump</requirement>
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10 <requirement type="package" version="1.95_4.8">r-rcurl</requirement>
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11 </requirements>
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12 <description>
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13 Download data with BDSS client and generate list (single end SRA data) and list:paired dataset collection
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14 (paired end SRA data).
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15 </description>
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16 <stdio>
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17 <!--All stderr are redirected to a file. "XXX" is used to match with nothing-->
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18 <regex match="XXX"
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19 source="stderr"
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20 level="warning"
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21 description="Check the warnings_and_errors.txt file for more details."/>
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22 </stdio>
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23 <command>
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24 <![CDATA[
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25 Rscript '${__tool_directory__}/bdss_client_sra_render.R'
a709a705ce09 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 813dcaa22f297814dd6d6a8c4c5ff01664942aa6-dirty
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26 -i '$sra_ids_se'
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27 -p '$sra_ids_pe'
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28 -f $format
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29 -e $echo
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31 -r $report
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32 -d $report.files_path
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33 -s $sink_message
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34
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35 -t '${__tool_directory__}/bdss_client_sra.Rmd'
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36 ]]>
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37 </command>
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38 <inputs>
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39 <param type="text" name="sra_ids_se" area="true" size="5x25" label="SRR/DRR/ERR accessions of single end SRA"
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40 help="A list of SRR/DRR/ERR accessions separated by comma or space. e.g. SRR039885"/>
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41 <param type="text" name="sra_ids_pe" area="true" size="5x25" label="SRR/DRR/ERR accessions of paired end SRA"
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42 help="A list of SRR/DRR/ERR accessions separated by comma or space. e.g. ERR1679739"/>
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43 <param type="boolean" name="format" truevalue="fastq" falsevalue="fasta" checked="true"
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44 label="output files in fastq (Yes) or fasta (No)?"/>
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45 <param type="boolean" name="echo" truevalue="TRUE" falsevalue="FALSE" checked="false"
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46 label="Display analysis code in report?"/>
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47 </inputs>
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48 <outputs>
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49 <data format="html" name="report" label="BDSS client report"/>
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50 <!--list dataset collection for single end SRA data-->
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51 <collection type="list" name="list_collection" label="BDSS download data (single end reads)">
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52 <discover_datasets pattern="__name_and_ext__" directory="se_read_files_directory"/>
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53 </collection>
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54 <!--list:paired dataset collection for paired end SRA data-->
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55 <collection type="list:paired" name="list:paired_collection" label="BDSS download data (paired end reads)">
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56 <discover_datasets
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57 pattern="(?P&lt;identifier_0&gt;[^_]+)_(?P&lt;identifier_1&gt;[^_]+)\.(?P&lt;ext&gt;[^\._]+)?"
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58 directory="pe_read_files_directory"/>
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59 </collection>
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60 <data format="txt" name="sink_message" label="Warnings and Errors" from_work_dir="warnings_and_errors.txt"/>
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61 </outputs>
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62 </tool>