Mercurial > repos > artbio > fetch_fasta_from_ncbi

annotate fetch_fasta_from_NCBI.xml @ 4:c667d0ee39f5 draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit ca3070e85c370b914ffa0562afe12b363e05aea4
author artbio
date Wed, 29 Nov 2017 17:38:52 -0500
parents 8be88084f89c
children 706fe8139955
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4
c667d0ee39f5 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit ca3070e85c370b914ffa0562afe12b363e05aea4
artbio
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diff changeset
1 <tool id="retrieve_fasta_from_NCBI" name="Retrieve FASTA from NCBI" version="2.3.0">
1
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
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2 <description></description>
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
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3 <command><![CDATA[
4
c667d0ee39f5 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit ca3070e85c370b914ffa0562afe12b363e05aea4
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4 python '$__tool_directory__'/fetch_fasta_from_NCBI.py
c667d0ee39f5 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit ca3070e85c370b914ffa0562afe12b363e05aea4
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5 -i "$queryString"
c667d0ee39f5 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit ca3070e85c370b914ffa0562afe12b363e05aea4
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6 -d $dbname
c667d0ee39f5 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit ca3070e85c370b914ffa0562afe12b363e05aea4
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7 -l '$logfile'
c667d0ee39f5 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit ca3070e85c370b914ffa0562afe12b363e05aea4
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8 -c
c667d0ee39f5 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit ca3070e85c370b914ffa0562afe12b363e05aea4
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9 -o '$outfile';
c667d0ee39f5 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit ca3070e85c370b914ffa0562afe12b363e05aea4
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10 #if $dry_run == ""
c667d0ee39f5 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit ca3070e85c370b914ffa0562afe12b363e05aea4
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11 number_UIDs=\$(tail -n 2 $logfile | perl -ne '/Found (\d+) UID/ && print \$1');
c667d0ee39f5 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit ca3070e85c370b914ffa0562afe12b363e05aea4
artbio
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12 python '$__tool_directory__'/fetch_fasta_from_NCBI.py
c667d0ee39f5 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit ca3070e85c370b914ffa0562afe12b363e05aea4
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13 -i "$queryString"
c667d0ee39f5 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit ca3070e85c370b914ffa0562afe12b363e05aea4
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14 -d $dbname
c667d0ee39f5 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit ca3070e85c370b914ffa0562afe12b363e05aea4
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15 -u
c667d0ee39f5 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit ca3070e85c370b914ffa0562afe12b363e05aea4
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16 -l '$logfile'
c667d0ee39f5 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit ca3070e85c370b914ffa0562afe12b363e05aea4
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17 -o 'uid_outfile';
c667d0ee39f5 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit ca3070e85c370b914ffa0562afe12b363e05aea4
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18 UID_array=( \$(head uid_outfile) );
c667d0ee39f5 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit ca3070e85c370b914ffa0562afe12b363e05aea4
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19 array_len=\${#UID_array[@]};
c667d0ee39f5 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit ca3070e85c370b914ffa0562afe12b363e05aea4
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20 counter=0;
c667d0ee39f5 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit ca3070e85c370b914ffa0562afe12b363e05aea4
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21 number_of_groups=\$((array_len / 200000));
c667d0ee39f5 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit ca3070e85c370b914ffa0562afe12b363e05aea4
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22 modulo=\$((array_len % 200000));
c667d0ee39f5 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit ca3070e85c370b914ffa0562afe12b363e05aea4
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23 if [ "\$modulo" -gt 0 ];then
c667d0ee39f5 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit ca3070e85c370b914ffa0562afe12b363e05aea4
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24 number_of_groups=\$((number_of_groups + 1));
c667d0ee39f5 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit ca3070e85c370b914ffa0562afe12b363e05aea4
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25 fi;
c667d0ee39f5 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit ca3070e85c370b914ffa0562afe12b363e05aea4
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26 group_number=1;
c667d0ee39f5 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit ca3070e85c370b914ffa0562afe12b363e05aea4
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27 echo "----- Number of groups of batches: \$number_of_groups -----" >> $logfile;
c667d0ee39f5 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit ca3070e85c370b914ffa0562afe12b363e05aea4
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28 for ((i=0; i+200000<array_len;i+=200000)); do
c667d0ee39f5 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit ca3070e85c370b914ffa0562afe12b363e05aea4
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29 echo "----- Group number: \$group_number -----" >> $logfile;
c667d0ee39f5 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit ca3070e85c370b914ffa0562afe12b363e05aea4
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30 echo "\${UID_array[@]:\$i:99999}" > uid_list_1.txt;
c667d0ee39f5 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit ca3070e85c370b914ffa0562afe12b363e05aea4
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31 echo "\${UID_array[@]:\$((i+100000)):99999}" > uid_list_2.txt;
c667d0ee39f5 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit ca3070e85c370b914ffa0562afe12b363e05aea4
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32 python '$__tool_directory__'/fetch_fasta_from_NCBI.py
c667d0ee39f5 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit ca3070e85c370b914ffa0562afe12b363e05aea4
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33 -d $dbname
c667d0ee39f5 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit ca3070e85c370b914ffa0562afe12b363e05aea4
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34 -l '$logfile'
c667d0ee39f5 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit ca3070e85c370b914ffa0562afe12b363e05aea4
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35 -o 'tmp1_outfile'
c667d0ee39f5 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit ca3070e85c370b914ffa0562afe12b363e05aea4
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36 --UID_list uid_list_1.txt&
c667d0ee39f5 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit ca3070e85c370b914ffa0562afe12b363e05aea4
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37 python '$__tool_directory__'/fetch_fasta_from_NCBI.py
c667d0ee39f5 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit ca3070e85c370b914ffa0562afe12b363e05aea4
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38 -d $dbname
c667d0ee39f5 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit ca3070e85c370b914ffa0562afe12b363e05aea4
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39 -l 'tmp1_logfile'
c667d0ee39f5 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit ca3070e85c370b914ffa0562afe12b363e05aea4
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40 -o 'tmp2_outfile'
c667d0ee39f5 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit ca3070e85c370b914ffa0562afe12b363e05aea4
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41 --UID_list uid_list_2.txt&
c667d0ee39f5 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit ca3070e85c370b914ffa0562afe12b363e05aea4
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42 wait;
c667d0ee39f5 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit ca3070e85c370b914ffa0562afe12b363e05aea4
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43 cat tmp1_outfile tmp2_outfile>> $outfile;
c667d0ee39f5 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit ca3070e85c370b914ffa0562afe12b363e05aea4
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44 rm tmp1_outfile tmp2_outfile;
c667d0ee39f5 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit ca3070e85c370b914ffa0562afe12b363e05aea4
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45 cat tmp1_logfile >> $logfile;
c667d0ee39f5 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit ca3070e85c370b914ffa0562afe12b363e05aea4
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46 rm tmp1_logfile;
c667d0ee39f5 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit ca3070e85c370b914ffa0562afe12b363e05aea4
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47 rm uid_list_1.txt uid_list_2.txt;
c667d0ee39f5 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit ca3070e85c370b914ffa0562afe12b363e05aea4
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48 group_number=\$((group_number + 1));
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49 counter=\$(( counter + 200000 ));
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50 done;
c667d0ee39f5 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit ca3070e85c370b914ffa0562afe12b363e05aea4
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51 echo "----- Group number: \$group_number -----" >> $logfile;
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52 echo "----- Last group -----" >> $logfile;
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53 if [ "\$counter" -lt "\$array_len" ]; then
c667d0ee39f5 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit ca3070e85c370b914ffa0562afe12b363e05aea4
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54 echo "\${UID_array[@]:\$counter:\$((array_len - counter + 1))}" > uid_list.txt;
c667d0ee39f5 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit ca3070e85c370b914ffa0562afe12b363e05aea4
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55 python '$__tool_directory__'/fetch_fasta_from_NCBI.py
c667d0ee39f5 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit ca3070e85c370b914ffa0562afe12b363e05aea4
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56 -d $dbname
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57 -l '$logfile'
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58 -o 'tmp_outfile'
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59 --UID_list uid_list.txt;
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60 rm uid_list.txt;
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61 cat tmp_outfile >> $outfile;
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62 rm tmp_outfile;
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63 fi;
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64 #end if
1
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65 ]]></command>
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66
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67 <inputs>
4
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68 <param name="queryString" type="text" size="5x80" area="True" value="txid10239[orgn] NOT txid131567[orgn] AND complete[all] NOT partial[title] NOT phage[title]" label="Query to NCBI in entrez format" help="exemple: Drosophila melanogaster[Organism] AND Gcn5[Title]">
1
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69 <sanitizer>
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70 <valid initial="string.printable">
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71 <remove value="&quot;"/>
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72 <remove value="\"/>
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73 </valid>
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74 <mapping initial="none">
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75 <add source="&quot;" target="\&quot;"/>
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76 <add source="\" target="\\"/>
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77 </mapping>
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78 </sanitizer>
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79 </param>
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80 <param name="dbname" type="select" label="NCBI database">
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81 <option value="nuccore">Nucleotide</option>
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82 <option value="protein">Protein</option>
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83 </param>
4
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84 <param name="dry_run" type="boolean" label="Get only the number of sequences" truevalue="--count" falsevalue="" checked="false"/>
1
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85 </inputs>
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86 <outputs>
3
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87 <data name="outfile" format="fasta" label="${tool.name} (${dbname.value_label}) with queryString '${queryString.value}'" >
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88 <filter> dry_run == False</filter>
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89 </data>
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90 <data format="txt" name="logfile" label="${tool.name}: log"/>
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91 </outputs>
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92 <tests>
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93 <test>
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94 <param name="queryString" value="9629650[gi]" />
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95 <param name="dbname" value="nuccore" />
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96 <output name="outfilename" ftype="fasta" file="output.fa" />
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97 </test>
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98 <test>
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99 <param name="queryString" value="CU929326[Accession]" />
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100 <param name="dbname" value="nuccore" />
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101 <param name="date_filter" value="1"/>
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102 <param name="dry_run" value="True"/>
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103 <output name="logfile" ftype="txt" file="dry_run.log" compare="sim_size"/>
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104 </test>
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105 <test>
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106 <param name="queryString" value="Drosophila[Organism] AND 2014[PDAT] AND virus" />
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107 <output name="outfilename" ftype="fasta" >
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108 <metadata name="sequences" value="13" />
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109 </output>
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110 </test>
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111 </tests>
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112 <help>
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113 **What it does**
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114
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115 This tool retrieves nucleotide/peptide sequences from the corresponding NCBI database (nuccore or protein) for a given entrez query.
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116
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117 The tool is preset with "txid10239[orgn] NOT txid131567[orgn] AND complete NOT partial[title] NOT phage[title]" for metaVisitor use purpose
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118
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119 See `Entrez help`_ for explanation of query formats
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120
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121 Be sure to use the appropriate NCBI query syntax. Always use [] to specify the search fields.
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122
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123 By checking the checkbox you can also run your query without sequence retrieval and get the number of sequences your query will fetch.
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124
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125 Note that the tool may fail in case of interrupted connexion with the NCBI database (see the log dataset)
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126
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127 Retrieval progress is reported in the log dataset.
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128
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129 **Acknowledgments**
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130
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131 This Galaxy tool has been adapted from the galaxy tool `get_fasta_from_taxon`_.
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132
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133 It is Copyright © 2014-2015 `CNRS and University Pierre et Marie Curie`_ and is released under the `MIT license`_.
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134
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135 .. _Entrez help: https://www.ncbi.nlm.nih.gov/books/NBK3837/#EntrezHelp.Entrez_Searching_Options
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136 .. _get_fasta_from_taxon: https://toolshed.g2.bx.psu.edu/view/crs4/get_fasta_from_taxon
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137 .. _CNRS and University Pierre et Marie Curie: http://www.ibps.upmc.fr/en
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138 .. _MIT license: http://opensource.org/licenses/MIT
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139
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140 </help>
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141 <citations>
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142 <citation type="doi">10.1186/1471-2105-14-73</citation>
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143 </citations>
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144 </tool>