Mercurial > repos > ebi-gxa > atlas_fastq_provider
annotate fastq_provider.xml @ 0:22ce1e7f1aaa draft default tip
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/fastq_provider commit 507503548ba8b4c5b7fd3dc93e63d9669b8e8e57"
author | ebi-gxa |
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date | Wed, 09 Mar 2022 12:58:37 +0000 |
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0
22ce1e7f1aaa
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/fastq_provider commit 507503548ba8b4c5b7fd3dc93e63d9669b8e8e57"
ebi-gxa
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1 <tool id="fastq_provider" name="Atlas FASTQ provider" version="@TOOL_VERSION@+galaxy" python_template_version="3.5" profile="20.01"> |
22ce1e7f1aaa
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/fastq_provider commit 507503548ba8b4c5b7fd3dc93e63d9669b8e8e57"
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2 <description> Retrieval and download of FASTQ files from ENA and other repositories such as HCA. The tool is used in production pipelines of EMBL-EBI Expression Atlas and Single Cell Expression Atlas. </description> |
22ce1e7f1aaa
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/fastq_provider commit 507503548ba8b4c5b7fd3dc93e63d9669b8e8e57"
ebi-gxa
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3 <macros> |
22ce1e7f1aaa
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/fastq_provider commit 507503548ba8b4c5b7fd3dc93e63d9669b8e8e57"
ebi-gxa
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4 <token name="@TOOL_VERSION@">0.4.2</token> |
22ce1e7f1aaa
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/fastq_provider commit 507503548ba8b4c5b7fd3dc93e63d9669b8e8e57"
ebi-gxa
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5 </macros> |
22ce1e7f1aaa
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/fastq_provider commit 507503548ba8b4c5b7fd3dc93e63d9669b8e8e57"
ebi-gxa
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6 <requirements> |
22ce1e7f1aaa
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/fastq_provider commit 507503548ba8b4c5b7fd3dc93e63d9669b8e8e57"
ebi-gxa
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7 <requirement type="package" version="@TOOL_VERSION@">atlas-fastq-provider</requirement> |
22ce1e7f1aaa
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/fastq_provider commit 507503548ba8b4c5b7fd3dc93e63d9669b8e8e57"
ebi-gxa
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8 </requirements> |
22ce1e7f1aaa
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/fastq_provider commit 507503548ba8b4c5b7fd3dc93e63d9669b8e8e57"
ebi-gxa
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9 <command detect_errors="exit_code"><![CDATA[ |
22ce1e7f1aaa
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/fastq_provider commit 507503548ba8b4c5b7fd3dc93e63d9669b8e8e57"
ebi-gxa
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10 fetchFastq.sh -f '$source' -t '$target' |
22ce1e7f1aaa
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/fastq_provider commit 507503548ba8b4c5b7fd3dc93e63d9669b8e8e57"
ebi-gxa
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11 #if $resource |
22ce1e7f1aaa
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/fastq_provider commit 507503548ba8b4c5b7fd3dc93e63d9669b8e8e57"
ebi-gxa
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12 -s '$resource' |
22ce1e7f1aaa
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/fastq_provider commit 507503548ba8b4c5b7fd3dc93e63d9669b8e8e57"
ebi-gxa
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13 #end if |
22ce1e7f1aaa
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/fastq_provider commit 507503548ba8b4c5b7fd3dc93e63d9669b8e8e57"
ebi-gxa
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14 #if $retrieval_method |
22ce1e7f1aaa
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/fastq_provider commit 507503548ba8b4c5b7fd3dc93e63d9669b8e8e57"
ebi-gxa
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15 -m '$retrieval_method' |
22ce1e7f1aaa
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/fastq_provider commit 507503548ba8b4c5b7fd3dc93e63d9669b8e8e57"
ebi-gxa
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16 #end if |
22ce1e7f1aaa
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/fastq_provider commit 507503548ba8b4c5b7fd3dc93e63d9669b8e8e57"
ebi-gxa
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17 #if $mode |
22ce1e7f1aaa
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/fastq_provider commit 507503548ba8b4c5b7fd3dc93e63d9669b8e8e57"
ebi-gxa
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18 -p '$mode' |
22ce1e7f1aaa
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/fastq_provider commit 507503548ba8b4c5b7fd3dc93e63d9669b8e8e57"
ebi-gxa
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19 #end if |
22ce1e7f1aaa
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/fastq_provider commit 507503548ba8b4c5b7fd3dc93e63d9669b8e8e57"
ebi-gxa
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20 #if $library |
22ce1e7f1aaa
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/fastq_provider commit 507503548ba8b4c5b7fd3dc93e63d9669b8e8e57"
ebi-gxa
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21 -l '$library' |
22ce1e7f1aaa
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/fastq_provider commit 507503548ba8b4c5b7fd3dc93e63d9669b8e8e57"
ebi-gxa
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22 #end if |
22ce1e7f1aaa
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/fastq_provider commit 507503548ba8b4c5b7fd3dc93e63d9669b8e8e57"
ebi-gxa
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23 #if $config_file |
22ce1e7f1aaa
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/fastq_provider commit 507503548ba8b4c5b7fd3dc93e63d9669b8e8e57"
ebi-gxa
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24 -c '$config_file' |
22ce1e7f1aaa
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/fastq_provider commit 507503548ba8b4c5b7fd3dc93e63d9669b8e8e57"
ebi-gxa
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25 #end if |
22ce1e7f1aaa
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/fastq_provider commit 507503548ba8b4c5b7fd3dc93e63d9669b8e8e57"
ebi-gxa
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26 #if $validate_only |
22ce1e7f1aaa
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/fastq_provider commit 507503548ba8b4c5b7fd3dc93e63d9669b8e8e57"
ebi-gxa
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27 -v '$validate_only' |
22ce1e7f1aaa
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/fastq_provider commit 507503548ba8b4c5b7fd3dc93e63d9669b8e8e57"
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28 #end if |
22ce1e7f1aaa
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/fastq_provider commit 507503548ba8b4c5b7fd3dc93e63d9669b8e8e57"
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29 #if $download_type |
22ce1e7f1aaa
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/fastq_provider commit 507503548ba8b4c5b7fd3dc93e63d9669b8e8e57"
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30 -d '$download_type' |
22ce1e7f1aaa
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/fastq_provider commit 507503548ba8b4c5b7fd3dc93e63d9669b8e8e57"
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31 #end if |
22ce1e7f1aaa
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/fastq_provider commit 507503548ba8b4c5b7fd3dc93e63d9669b8e8e57"
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32 ; mv -f '$target' '$outfile' |
22ce1e7f1aaa
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/fastq_provider commit 507503548ba8b4c5b7fd3dc93e63d9669b8e8e57"
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33 ]]></command> |
22ce1e7f1aaa
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/fastq_provider commit 507503548ba8b4c5b7fd3dc93e63d9669b8e8e57"
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34 <inputs> |
22ce1e7f1aaa
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/fastq_provider commit 507503548ba8b4c5b7fd3dc93e63d9669b8e8e57"
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35 <param name="source" argument="-f" type="text" label="file or uri" help="file or uri" /> |
22ce1e7f1aaa
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/fastq_provider commit 507503548ba8b4c5b7fd3dc93e63d9669b8e8e57"
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36 <param name="target" argument="-t" type="text" label="target file" help="target file. E.g 'ERR035229.fastq.gz' " /> |
22ce1e7f1aaa
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/fastq_provider commit 507503548ba8b4c5b7fd3dc93e63d9669b8e8e57"
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37 <param name="resource" argument="-s" type="select" label="resource or directory, default 'auto' " help="How to fetch the file, e.g. there’s a specific method for getting results from the Human Cell Atlas' 'Azul' resource. " optional='true' > |
22ce1e7f1aaa
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/fastq_provider commit 507503548ba8b4c5b7fd3dc93e63d9669b8e8e57"
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38 <option value="auto" selected="true">auto</option> |
22ce1e7f1aaa
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/fastq_provider commit 507503548ba8b4c5b7fd3dc93e63d9669b8e8e57"
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39 <option value="ena">ENA</option> |
22ce1e7f1aaa
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/fastq_provider commit 507503548ba8b4c5b7fd3dc93e63d9669b8e8e57"
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40 <option value="sra">SRA file</option> |
22ce1e7f1aaa
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/fastq_provider commit 507503548ba8b4c5b7fd3dc93e63d9669b8e8e57"
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41 <option value="hca">Human Cell Atlas</option> |
22ce1e7f1aaa
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/fastq_provider commit 507503548ba8b4c5b7fd3dc93e63d9669b8e8e57"
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42 <option value="dir">Local directory</option> |
22ce1e7f1aaa
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/fastq_provider commit 507503548ba8b4c5b7fd3dc93e63d9669b8e8e57"
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43 </param> |
22ce1e7f1aaa
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/fastq_provider commit 507503548ba8b4c5b7fd3dc93e63d9669b8e8e57"
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44 <param name="retrieval_method" argument="-m" type="select" label="retrieval method, default 'wget' " help="retrieval method, default 'auto'. Files with hca source will use the 'hca' download method regardless (-m has no effect). Private ENA files will be fetched via 'ssh' (-m has no effect). The 'http' method refers to an HTTP endpoint in the EBI Fire resource. " optional='true'> |
22ce1e7f1aaa
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/fastq_provider commit 507503548ba8b4c5b7fd3dc93e63d9669b8e8e57"
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45 <option value="auto" selected="true">auto</option> |
22ce1e7f1aaa
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/fastq_provider commit 507503548ba8b4c5b7fd3dc93e63d9669b8e8e57"
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46 <option value="wget">wget</option> |
22ce1e7f1aaa
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/fastq_provider commit 507503548ba8b4c5b7fd3dc93e63d9669b8e8e57"
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47 <option value="dir">Local directory</option> |
22ce1e7f1aaa
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/fastq_provider commit 507503548ba8b4c5b7fd3dc93e63d9669b8e8e57"
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48 <option value="ssh">SSH (ENA files, for EBI only)</option> |
22ce1e7f1aaa
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/fastq_provider commit 507503548ba8b4c5b7fd3dc93e63d9669b8e8e57"
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49 <option value="http">HTTP endpoint (ENA files, EBI only)</option> |
22ce1e7f1aaa
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/fastq_provider commit 507503548ba8b4c5b7fd3dc93e63d9669b8e8e57"
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50 </param> |
22ce1e7f1aaa
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/fastq_provider commit 507503548ba8b4c5b7fd3dc93e63d9669b8e8e57"
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51 <param name="mode" argument="-p" type="select" label="public or private, default public. Private usable by EBI staff only" help="public or private, default 'public' " optional='true'> |
22ce1e7f1aaa
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/fastq_provider commit 507503548ba8b4c5b7fd3dc93e63d9669b8e8e57"
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52 <option value="public" selected="true">public</option> |
22ce1e7f1aaa
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/fastq_provider commit 507503548ba8b4c5b7fd3dc93e63d9669b8e8e57"
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53 <option value="private">private</option> |
22ce1e7f1aaa
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/fastq_provider commit 507503548ba8b4c5b7fd3dc93e63d9669b8e8e57"
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54 </param> |
22ce1e7f1aaa
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/fastq_provider commit 507503548ba8b4c5b7fd3dc93e63d9669b8e8e57"
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55 <param name="library" argument="-l" type="text" label="ENA library (ENA source files only), by default inferred from file name" help="library, by default inferred from file name. E.g. -l ERR1888646 " optional='true'/> |
22ce1e7f1aaa
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/fastq_provider commit 507503548ba8b4c5b7fd3dc93e63d9669b8e8e57"
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56 <param name="config_file" argument="-c" type="data" format="atlas-fastq-provider-config.sh" label="config file to override defaults" help="config file to override defaults" optional='true'/> |
22ce1e7f1aaa
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/fastq_provider commit 507503548ba8b4c5b7fd3dc93e63d9669b8e8e57"
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57 <param name="validate_only" argument="-v" type="boolean" label="validate only to check a source URI is valid, don't download" help="validate only, don't download" optional='true'/> |
22ce1e7f1aaa
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/fastq_provider commit 507503548ba8b4c5b7fd3dc93e63d9669b8e8e57"
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58 <param name="download_type" argument="-d" type="select" label="download type, fastq or SRA file" help="download type, fastq or srr" optional='true'> |
22ce1e7f1aaa
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/fastq_provider commit 507503548ba8b4c5b7fd3dc93e63d9669b8e8e57"
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59 <option value="fastq" selected="true">fastq</option> |
22ce1e7f1aaa
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/fastq_provider commit 507503548ba8b4c5b7fd3dc93e63d9669b8e8e57"
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60 <option value="srr">SRA</option> |
22ce1e7f1aaa
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/fastq_provider commit 507503548ba8b4c5b7fd3dc93e63d9669b8e8e57"
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61 </param> |
22ce1e7f1aaa
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/fastq_provider commit 507503548ba8b4c5b7fd3dc93e63d9669b8e8e57"
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62 </inputs> |
22ce1e7f1aaa
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/fastq_provider commit 507503548ba8b4c5b7fd3dc93e63d9669b8e8e57"
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63 <outputs> |
22ce1e7f1aaa
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/fastq_provider commit 507503548ba8b4c5b7fd3dc93e63d9669b8e8e57"
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64 <data name="outfile" label="${tool.name} on ${on_string}: compressed fastq file" format="fastq.gz" /> |
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"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/fastq_provider commit 507503548ba8b4c5b7fd3dc93e63d9669b8e8e57"
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65 </outputs> |
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66 <tests> |
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67 <test expect_num_outputs="1"> |
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68 <param name="source" value="ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR035/ERR035229/ERR035229.fastq.gz"/> |
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69 <param name="target" value="ERR035229.fastq.gz"/> |
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70 <output name="outfile" md5="c9482e89552630084997112787a5d796" /> |
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71 </test> |
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72 </tests> |
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73 <help><![CDATA[ |
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74 |
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75 Usage: fetchFastq.sh [-f <file or uri>] [-t <target file>] [-s <source resource or directory, default 'auto'>] [-m <retrieval method, default 'auto'>] [-p <public or private, default 'public'>] [-l <library, by default inferred from file name>] [-c <config file to override defaults>] [-v <validate only, don't download>] [-d <download type, 'fastq' or 'srr'>] |
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76 |
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77 ]]></help> |
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78 <citations> |
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79 <citation type="bibtex"> |
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80 @misc{githubatlas-fastq-provider, |
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81 author = {Jonathan Manning, EBI Gene Expression Team}, |
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82 year = {2021}, |
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83 title = {atlas-fastq-provider}, |
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84 publisher = {GitHub}, |
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85 journal = {GitHub repository}, |
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86 url = {https://github.com/ebi-gene-expression-group/atlas-fastq-provider}, |
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87 }</citation> |
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88 </citations> |
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89 </tool> |
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90 |