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annotate sra_pileup.xml @ 5:6f68b86da01a draft default tip

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planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit d754d6a6fc019236513d2228542fe1a2757d55cf-dirty
author mvdbeek
date Wed, 30 Sep 2015 11:47:04 -0400
parents 68527898a9ea
children
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68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
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1 <tool id="sra_pileup" name="Generate pileup format" version="1.2.4">
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
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2 <description>from NCBI sra.</description>
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3 <macros>
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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>
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6 <expand macro="requirements"/>
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7 <command>
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8 <![CDATA[
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
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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
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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
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11 ## with a cluster manager.
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
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12 export HOME=\$PWD;
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
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13 vdb-config --restore-defaults;
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
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14 vdb-config -s "/repository/user/main/public/root=\$PWD";
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
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15 #if ( str( $region ) == "" ):
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
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16 ASCP_PATH=`which ascp`;
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
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17 ASCP_KEY=`dirname \$ASCP_PATH`/asperaweb_id_dsa.openssh;
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
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18 prefetch --ascp-path "\$ASCP_PATH|\$ASCP_KEY" "$input.accession";
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
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19 ##Duplicate vdb-config, in case settings changed between prefetch and
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
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20 ##dump command.
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
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21 #end if
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
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22 vdb-config -s "/repository/user/main/public/root=\$PWD";
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
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23 sra-pileup --log-level fatal
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
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24 #if str( $region ) != "":
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
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25
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26 --aligned-region "$region"
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27
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28 #end if
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
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29 #if str( $minMapq ) != "":
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
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30 --minmapq "$minMapq"
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31 #end if
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
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32 #if $input.input_select == "file":
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
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33 "$input.file" > "$output_file"
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34 #elif $input.input_select == "accession_number":
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
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35 "$input.accession" > "$output_accession"
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
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36 #elif $input.input_select == "text":
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
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37 `cat $input.text` > "$output_text"
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
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38 #end if
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
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39 ]]>
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
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40 </command>
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
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41 <version_string>sra-pileup --version</version_string>
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
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42 <inputs>
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
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43 <conditional name="input">
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
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44 <param name="input_select" type="select" label="select input type">
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
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45 <option value="accession_number">SRR accession</option>
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
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46 <option value="file">SRA archive in current history</option>
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
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47 <option value="text">text file containing SRR accession</option>
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
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48 </param>
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
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49 <when value="file">
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50 <param format="sra" name="file" type="data" label="sra archive"/>
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51 </when>
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
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52 <when value="accession_number">
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
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53 <param format="text" name="accession" type="text" label="accession"/>
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54 </when>
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55 <when value="text">
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56 <param format="txt" name="text" type="data" label="text file"/>
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57 </when>
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58 </conditional>
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59 <expand macro="region"/>
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60 <expand macro="minMapq"/>
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61 </inputs>
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62 <outputs>
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63 <data format="pileup" name="output_accession" label="${input.accession}.pileup">
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64 <filter>input['input_select'] == "accession_number"</filter>
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65 </data>
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66 <data format="pileup" name="output_file" label="${input.file.name}.pileup">
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67 <filter>input['input_select'] == "file"</filter>
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68 </data>
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69 <data format="pileup" name="output_text" label="${input.text.name}.pileup">
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70 <filter>input['input_select'] == "text"</filter>
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71 </data>
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72 </outputs>
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73 <tests>
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74 <test>
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75 <param name="input_select" value="accession_number"/>
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76 <param name="accession" value="SRR925743"/>
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77 <param name="region" value="17:41243452-41277500"/>
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78 <output name="output_accession" file="sra_pileup_result.pileup" ftype="pileup"/>
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79 </test>
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80 </tests>
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81 <help>
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82 This tool produces pileup format from sra archives using sra-pileup.
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83 The sra-pileup program is developed at NCBI, and is available at
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84 http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software.
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85 @SRATOOLS_ATTRRIBUTION@
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86 </help>
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87 </tool>