Mercurial > repos > iuc > ncbi_acc_download

annotate ncbi_acc_download.xml @ 0:1c58de56d587 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
author iuc
date Wed, 04 Dec 2019 07:01:37 -0500
parents
children e063168e0a81
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0
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
1 <tool id="ncbi_acc_download" name="NCBI Accession Download" version="@TOOL_VERSION@+galaxy0">
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
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2 <description>Download sequences from GenBank/RefSeq by accession through the NCBI ENTREZ API</description>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
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3 <macros>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
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4 <import>macros.xml</import>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
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5 </macros>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
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6 <requirements>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
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7 <requirement type="package" version="@TOOL_VERSION@">ncbi-acc-download</requirement>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
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8 </requirements>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
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9 <command detect_errors="exit_code"><![CDATA[
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
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10 #if $query_source.select == "accession_file":
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
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11 { grep -v "^[ \t]*$" $query_source.accession_file > accessions ||
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
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12 { echo "No accession numbers in input. Aborting." 1>&2; exit 1; } } &&
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
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13 #else if $query_source.select == "accession_list":
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
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14 echo '$query_source.accession_list' | sed -r 's/(\,|__cn__)/\n/g' | grep -v "^[ \t]*$" > accessions &&
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
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15 #end if
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
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16 mkdir outdir &&
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
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17 cd outdir &&
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
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18 ignore_errors=$ignore_failed &&
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
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19 while read accession; do
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
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20 echo "Downloading accession number: " \$accession " ..." >> ../error.log &&
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
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21 ncbi-acc-download
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
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22 --molecule '${molecule.select}'
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
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23 --format '${molecule.format}'
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
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24 #if $molecule.format != 'featuretable' and $molecule.format != 'gff3':
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
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25 --extended-validation all
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
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26 #end if
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
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27 \${accession};
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
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28 failure=\$?;
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
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29 if [ \$failure -ne 0 ]; then
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
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30 echo " failed." >> ../error.log;
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
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31 if [ \$ignore_errors -ne 0 ]; then
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
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32 echo \$accession >> ../failed.txt;
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
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33 else
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
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34 exit 1;
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
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35 fi;
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
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36 else
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
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37 echo " done." >> ../error.log;
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
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38 fi;
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
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39 sleep 2;
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
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40 done < ../accessions 2> >(tee -a ../error.log >&2);
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
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41 ]]></command>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
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42 <inputs>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
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43 <conditional name="query_source">
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
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44 <param name="select" type="select" label="Select source for IDs">
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
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45 <option value="accession_file">File containing Accessions (one per line)</option>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
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46 <option value="accession_list">Direct Entry</option>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
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47 </param>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
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48 <when value="accession_file">
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
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49 <param label="Accession File" name="accession_file" type="data" format="txt,tabular"/>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
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50 </when>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
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51 <when value="accession_list">
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
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52 <param label="ID List" name="accession_list" type="text" area="true" help="Newline/Comma separated list of IDs">
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
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53 <validator type="expression" message="ID list cannot be empty">value.strip()</validator>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
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54 </param>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
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55 </when>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
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56 </conditional>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
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57 <conditional name="molecule">
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
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58 <param name="select" type="select" label="Molecule Type">
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
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59 <option value="nucleotide" selected="true">Nucleotide</option>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
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60 <option value="protein">Protein</option>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
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61 </param>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
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62 <when value="nucleotide">
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
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63 <param name="format" type="select" label="File Format">
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
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64 <option value="fasta" selected="true">FASTA</option>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
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65 <option value="genbank">GenBank</option>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
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66 <option value="featuretable">Feature Table</option>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
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67 <option value="gff3">GFF3</option>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
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68 </param>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
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69 </when>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
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70 <when value="protein">
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
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71 <param name="format" type="select" label="File Format">
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
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72 <option value="fasta" selected="true">FASTA</option>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
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73 </param>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
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74 </when>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
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75 </conditional>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
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76 <param name="ignore_failed" type="select" display="radio"
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
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77 label="How to handle download failures">
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
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78 <option value="0">Abort with error on first failure</option>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
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79 <option value="1">Add accession to failed list and continue</option>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
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80 </param>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
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81 </inputs>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
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82 <outputs>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
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parents:
diff changeset
83 <collection name="output" type="list" label="${tool.name} on ${on_string}: Downloaded Files">
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
84 <discover_datasets pattern="(?P&lt;name&gt;.+)\.fa$" directory="outdir" format="fasta"/>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
85 <discover_datasets pattern="(?P&lt;name&gt;.+)\.gbk$" directory="outdir" format="genbank"/>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
86 <discover_datasets pattern="(?P&lt;name&gt;.+)\.gff$" directory="outdir" format="gff"/>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
87 <discover_datasets pattern="(?P&lt;name&gt;.+)\.ft$" directory="outdir" format="txt"/>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
88 </collection>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
89 <data name="error_log" from_work_dir="error.log" label="${tool.name} on ${on_string}: Log" format="txt"/>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
90 <data name="failed_accessions" from_work_dir="failed.txt" label="${tool.name} on ${on_string}: Failed accessions" format="txt">
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
91 <filter>str(ignore_failed)=='1'</filter>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
92 </data>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
93 </outputs>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
94 <tests>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
95 <test>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
96 <conditional name="molecule">
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
97 <param name="select" value="nucleotide"/>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
98 <param name="format" value="fasta"/>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
99 </conditional>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
100 <conditional name="query_source">
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
101 <param name="select" value="accession_file" />
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
102 <param name="accession_file" value="accessions_1.tsv"/>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
103 </conditional>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
104 <output_collection name="output" type="list">
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
105 <element name="CP011064" ftype="fasta">
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
106 <assert_contents>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
107 <has_line line=">CP011064.1 Escherichia coli str. Sanji plasmid pSJ_94, complete sequence" />
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
108 </assert_contents>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
109 </element>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
110 <element name="CP021680" ftype="fasta">
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
111 <assert_contents>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
112 <has_line line=">CP021680.1 Escherichia coli strain AR_0162 plasmid tig00002623, complete sequence" />
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
113 </assert_contents>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
114 </element>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
115 </output_collection>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
116 </test>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
117 <test>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
118 <conditional name="molecule">
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
119 <param name="select" value="nucleotide"/>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
120 <param name="format" value="genbank"/>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
121 </conditional>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
122 <conditional name="query_source">
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
123 <param name="select" value="accession_file" />
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
124 <param name="accession_file" value="accessions_1.tsv"/>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
125 </conditional>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
126 <output_collection name="output" type="list">
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
127 <element name="CP011064" ftype="genbank">
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
128 <assert_contents>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
129 <has_line line="DEFINITION Escherichia coli str. Sanji plasmid pSJ_94, complete sequence." />
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
130 </assert_contents>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
131 </element>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
132 <element name="CP021680" ftype="genbank">
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
133 <assert_contents>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
134 <has_line line="DEFINITION Escherichia coli strain AR_0162 plasmid tig00002623, complete" />
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
135 </assert_contents>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
136 </element>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
137 </output_collection>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
138 </test>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
139 <test>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
140 <conditional name="molecule">
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
141 <param name="select" value="nucleotide"/>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
142 <param name="format" value="gff3"/>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
143 </conditional>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
144 <conditional name="query_source">
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
145 <param name="select" value="accession_file" />
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
146 <param name="accession_file" value="accessions_1.tsv"/>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
147 </conditional>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
148 <output_collection name="output" type="list">
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
149 <element name="CP011064" ftype="gff">
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
150 <assert_contents>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
151 <has_line line="##sequence-region CP011064.1 1 94712" />
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
152 </assert_contents>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
153 </element>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
154 <element name="CP021680" ftype="gff">
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
155 <assert_contents>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
156 <has_line line="##sequence-region CP021680.1 1 23332" />
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
157 </assert_contents>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
158 </element>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
159 </output_collection>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
160 </test>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
161 <test>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
162 <conditional name="molecule">
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
163 <param name="select" value="nucleotide"/>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
164 <param name="format" value="featuretable"/>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
165 </conditional>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
166 <conditional name="query_source">
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
167 <param name="select" value="accession_file" />
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
168 <param name="accession_file" value="accessions_1.tsv"/>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
169 </conditional>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
170 <output_collection name="output" type="list">
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
171 <element name="CP011064" ftype="txt">
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
172 <assert_contents>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
173 <has_line line=">Feature gb|CP011064.1|" />
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
174 </assert_contents>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
175 </element>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
176 <element name="CP021680" ftype="txt">
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
177 <assert_contents>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
178 <has_line line=">Feature gb|CP021680.1|" />
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
179 </assert_contents>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
180 </element>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
181 </output_collection>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
182 </test>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
183 <test>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
184 <conditional name="molecule">
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
185 <param name="select" value="nucleotide"/>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
186 <param name="format" value="fasta"/>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
187 </conditional>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
188 <conditional name="query_source">
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
189 <param name="select" value="accession_list" />
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
190 <param name="accession_list" value="CP011064,CP021680"/>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
191 </conditional>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
192 <output_collection name="output" type="list">
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
193 <element name="CP011064" ftype="fasta">
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
194 <assert_contents>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
195 <has_line line=">CP011064.1 Escherichia coli str. Sanji plasmid pSJ_94, complete sequence" />
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
196 </assert_contents>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
197 </element>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
198 <element name="CP021680" ftype="fasta">
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
199 <assert_contents>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
200 <has_line line=">CP021680.1 Escherichia coli strain AR_0162 plasmid tig00002623, complete sequence" />
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
201 </assert_contents>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
202 </element>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
203 </output_collection>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
204 </test>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
205 <test>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
206 <conditional name="molecule">
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
207 <param name="select" value="nucleotide"/>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
208 <param name="format" value="fasta"/>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
209 </conditional>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
210 <conditional name="query_source">
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
211 <param name="select" value="accession_list" />
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
212 <param name="accession_list" value="CP011064,CP0XXXXX,CP021680"/>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
213 </conditional>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
214 <param name="ignore_failed" value="1" />
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
215 <output_collection name="output" type="list">
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
216 <element name="CP011064" ftype="fasta">
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
217 <assert_contents>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
218 <has_line line=">CP011064.1 Escherichia coli str. Sanji plasmid pSJ_94, complete sequence" />
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
219 </assert_contents>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
220 </element>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
221 <element name="CP021680" ftype="fasta">
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
222 <assert_contents>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
223 <has_line line=">CP021680.1 Escherichia coli strain AR_0162 plasmid tig00002623, complete sequence" />
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
224 </assert_contents>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
225 </element>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
226 </output_collection>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
227 <output name="failed_accessions">
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
228 <assert_contents>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
229 <has_line line="CP0XXXXX" />
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
230 </assert_contents>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
231 </output>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
232 </test>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
233 <test>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
234 <conditional name="molecule">
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
235 <param name="select" value="nucleotide"/>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
236 <param name="format" value="fasta"/>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
237 </conditional>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
238 <conditional name="query_source">
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
239 <param name="select" value="accession_list" />
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
240 <param name="accession_list" value="CP0XXXXX"/>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
241 </conditional>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
242 <param name="ignore_failed" value="1" />
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
243 <output name="failed_accessions">
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
244 <assert_contents>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
245 <has_line line="CP0XXXXX" />
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
246 </assert_contents>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
247 </output>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
248 </test>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
249 <test expect_failure="true">
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
250 <conditional name="molecule">
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
251 <param name="select" value="nucleotide"/>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
iuc
parents:
diff changeset
252 <param name="format" value="fasta"/>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
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253 </conditional>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
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254 <conditional name="query_source">
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
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255 <param name="select" value="accession_list" />
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
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256 <param name="accession_list" value="CP011064,CP0XXXXX,CP021680"/>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
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257 </conditional>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
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258 <param name="ignore_failed" value="0" />
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
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259 </test>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
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260 <test>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
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261 <conditional name="molecule">
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
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262 <param name="select" value="nucleotide"/>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
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263 <param name="format" value="fasta"/>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
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264 </conditional>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
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265 <conditional name="query_source">
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
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266 <param name="select" value="accession_list" />
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
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267 <param name="accession_list" value="CP011064&#10;CP021680"/>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
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268 </conditional>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
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269 <output_collection name="output" type="list">
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
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270 <element name="CP011064" ftype="fasta">
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
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271 <assert_contents>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
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272 <has_line line=">CP011064.1 Escherichia coli str. Sanji plasmid pSJ_94, complete sequence" />
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
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273 </assert_contents>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
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274 </element>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
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275 <element name="CP021680" ftype="fasta">
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
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276 <assert_contents>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
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277 <has_line line=">CP021680.1 Escherichia coli strain AR_0162 plasmid tig00002623, complete sequence" />
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
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278 </assert_contents>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
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279 </element>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
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280 </output_collection>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
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281 </test>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
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282 <test>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
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283 <conditional name="molecule">
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
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284 <param name="select" value="protein"/>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
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285 <param name="format" value="fasta"/>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
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286 </conditional>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
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287 <conditional name="query_source">
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
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288 <param name="select" value="accession_list" />
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
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289 <param name="accession_list" value="NP_003192"/>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
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290 </conditional>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
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291 <output_collection name="output" type="list">
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
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292 <element name="NP_003192" ftype="fasta">
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
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293 <assert_contents>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
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294 <has_line line=">NP_003192.1 transcription factor A, mitochondrial isoform 1 precursor [Homo sapiens]" />
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
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295 </assert_contents>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
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296 </element>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
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297 </output_collection>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
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298 </test>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
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299 </tests>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
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300 <help><![CDATA[
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
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301 **What it does**
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
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302 Given a file containing a list of NCBI accession numbers or a direct entry of accession numbers in the tool text input box, this tool will download the corresponding sequence records via the NCBI API.
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
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303
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
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304 **Limitations**
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
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305 - For protein sequence downloads, only fasta format is supported
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
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306 - To avoid rate-limits imposed by the NCBI API, records are downloaded sequentially with a delay between requests. This may make it impractical to use this tool to download many (>100) records.
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
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307
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
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308 **Output**
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
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309 A collection of sequence records in the desired format.
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310 ]]></help>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
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311 <citations>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
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312 </citations>
1c58de56d587 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 6747338e8e02cb87c4f3b9cdea0b761f236a02d1"
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313 </tool>