Mercurial > repos > mvdbeek > sra_tools

annotate fastq_dump.xml @ 0:68527898a9ea draft

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planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
author mvdbeek
date Fri, 25 Sep 2015 09:28:56 -0400
parents
children 6f68b86da01a
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68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
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1 <tool id="fastq_dump" name="Extract reads" version="1.2.4">
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
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2 <description>in FASTQ/A format from NCBI SRA.</description>
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
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3 <macros>
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
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4 <import>sra_macros.xml</import>
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
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5 </macros>
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
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6 <expand macro="requirements"/>
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
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7 <command>
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
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8 <![CDATA[
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
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9 ## Need to set the home directory to the current working directory,
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
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10 ## else the tool tries to write to home/.ncbi and fails when used
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
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11 ## with a cluster manager.
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
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12 export HOME=\$PWD;
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
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13 vdb-config --restore-defaults;
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
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14 #if $input.input_select == "file":
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
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15 fastq-dump --log-level fatal --accession '${input.file.name}'
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
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16 #else:
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
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17 vdb-config -s "/repository/user/main/public/root=\$PWD";
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
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18 ## Do not use prefetch if region is specified, to avoid downloading
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
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19 ## the complete sra file.
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
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20 #if ( str( $region ) == "" ) and ( str( $minID ) == "" ) and ( str( $maxID ) == "" ):
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
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21 ASCP_PATH=`which ascp`;
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
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22 ASCP_KEY=`dirname \$ASCP_PATH`/asperaweb_id_dsa.openssh;
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
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23 prefetch --ascp-path "\$ASCP_PATH|\$ASCP_KEY" $input.accession;
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
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24 #end if
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
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25 ## Duplicate vdb-config, in case settings changed between prefetch and
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
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26 ## dump command.
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
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27 vdb-config -s "/repository/user/main/public/root=\$PWD";
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
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28 fastq-dump --accession "$input.accession"
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
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29 #end if
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
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30 --defline-seq '@\$sn[_\$rn]/\$ri'
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
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31 --stdout
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
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32 #if str( $split ) == "yes":
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
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33 --split-spot
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
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34 #end if
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
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35 #if str( $alignments ) == "aligned":
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
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36 --aligned
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
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37 #end if
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
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38 #if str( $alignments ) == "unaligned":
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
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39 --unaligned
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
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40 #end if
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
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41 #if str( $minID ) != "":
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
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42 --minSpotId "$minID"
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
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43 #end if
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
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44 #if str( $maxID ) != "":
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
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45 --maxSpotId "$maxID"
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
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46 #end if
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
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47 #if str( $minlen ) != "":
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
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48 --minReadLen "$minlen"
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
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49 #end if
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
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50 #if str( $readfilter ) != "":
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
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51 --read-filter "$readfilter"
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
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52 #end if
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
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53 #if str( $region ) != "":
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
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54 --aligned-region "$region"
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
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55 #end if
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
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56 #if str( $spotgroups ) != "":
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
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57 --spot-groups "$spotgroups"
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
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58 #end if
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
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59 #if str( $matepairDist ) != "":
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
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60 --matepair-distance "$matepairDist"
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
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61 #end if
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
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62 #if $clip == "yes":
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
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63 --clip
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
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64 #end if
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
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65 #if str( $outputformat ) == "fasta":
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
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66 --fasta
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
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67 #end if
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
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68 #if $input.input_select=="file":
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
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69 "$input.file" > "$output_file"
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
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70 #else:
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
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71 "$input.accession" > "$output_accession"
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
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72 #end if
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
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73 ]]>
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
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74 </command>
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
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75 <version_string>fastq-dump --version</version_string>
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
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76 <inputs>
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
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77 <expand macro="input_conditional"/>
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
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78 <param name="minID" type="integer" label="minimum spot ID" optional="true"/>
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
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79 <param name="maxID" type="integer" label="maximum spot ID" optional="true"/>
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
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80 <param name="minlen" type="integer" label="minimum read length" optional="true"/>
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
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81 <param name="split" type="select" value="yes">
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
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82 <label>split spot by read pairs</label>
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
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83 <option value="yes">Yes</option>
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
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84 <option value="no">No</option>
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
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85 </param>
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
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86 <expand macro="alignments"/>
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
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87 <expand macro="region"/>
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
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88 <expand macro="matepairDist"/>
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
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89 <param name="readfilter" type="select" value="">
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
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90 <label>filter by value</label>
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
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91 <option value="">None</option>
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
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92 <option value="pass">pass</option>
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
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93 <option value="reject">reject</option>
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
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94 <option value="criteria">criteria</option>
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
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95 <option value="redacted">redacted</option>
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
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96 </param>
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
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97 <param name="outputformat" type="select" label="select output format">
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
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98 <option value="fastqsanger">fastq</option>
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
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99 <option value="fasta">fasta</option>
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
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100 </param>
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
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101 <param name="spotgroups" type="text" label="filter by spot-groups" optional="true"/>
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
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102 <param name="clip" type="select" value="no">
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
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103 <label>apply left and right clips</label>
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
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104 <option value="no">No</option>
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105 <option value="yes">Yes</option>
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106 </param>
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107 </inputs>
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108 <outputs>
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109 <data format="fastq" name="output_accession" label="${input.accession}.${outputformat}">
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110 <filter>input['input_select'] == "accession_number"</filter>
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111 <change_format>
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112 <when input="outputformat" value="fasta" format="fasta"/>
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113 </change_format>
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114 </data>
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115 <data format="fastq" name="output_file" label="${input.file.name}.${outputformat}">
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116 <filter>input['input_select'] == "file"</filter>
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117 <change_format>
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118 <when input="outputformat" value="fasta" format="fasta"/>
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119 </change_format>
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120 </data>
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121 </outputs>
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122 <stdio>
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123 <exit_code range="127" level="fatal" description="Could not locate fastq-dump binary"/>
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124 </stdio>
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125 <tests>
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126 <test>
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127 <param name="input_select" value="accession_number"/>
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128 <param name="outputformat" value="fastqsanger"/>
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129 <param name="accession" value="SRR925743"/>
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130 <param name="maxID" value="5"/>
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131 <output name="output_accession" file="fastq_dump_result.fastq" ftype="fastq"/>
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132 </test>
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133 </tests>
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134 <help>
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135 This tool extracts reads from SRA archives using fastq-dump.
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136 The fastq-dump program is developed at NCBI, and is available at
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137 http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software.
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138 @SRATOOLS_ATTRRIBUTION@
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139 </help>
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140 </tool>