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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="sam_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 SAM or BAM 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
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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
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6 <expand macro="requirements"/>
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
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7 <command>
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
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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 ## Do not use prefetch if region is specified, to avoid downloading
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
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16 ## the complete sra file.
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
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17 #if ( str( $region ) == "" ):
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
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18 ASCP_PATH=`which ascp`;
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
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19 ASCP_KEY=`dirname \$ASCP_PATH`/asperaweb_id_dsa.openssh;
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
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20 prefetch --ascp-path "\$ASCP_PATH|\$ASCP_KEY" "$input.accession";
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
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21 ##Duplicate vdb-config, in case settings changed between prefetch and
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22 ##dump command.
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23 #end if
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
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24 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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25 sam-dump --log-level fatal --disable-multithreading
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
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26 #if str( $region ) != "":
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
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27 --aligned-region "$region"
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
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28 #end if
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29 #if str( $matepairDist ) != "":
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
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30 --matepair-distance "$matepairDist"
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
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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 str( $minMapq ) != "":
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
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33 --min-mapq "$minMapq"
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34 #end if
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35 #if str( $header ) == "yes":
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36 --header
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37 #else:
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
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38 --no-header
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
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39 #end if
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
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40 #if str( $alignments ) == "both":
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41 --unaligned
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
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42 #end if
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
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43 #if str( $alignments ) == "unaligned":
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44 --unaligned-spots-only
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45 #end if
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
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46 #if (str( $primary ) == "yes") and (str ( $alignments != "unaligned") ):
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
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47 --primary
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
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48 #end if
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
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49 #if $input.input_select == "file":
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
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50 "$input.file"
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51 #elif $input.input_select == "accession_number":
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52 "$input.accession"
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53 #end if
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54 #if str( $outputformat ) == "bam":
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55 | samtools view -Sb - 2> /dev/null
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56 #end if
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57 #if $input.input_select == "file":
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58 > "$output_file"
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59 #elif $input.input_select == "accession_number":
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60 > "$output_accession"
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61 #end if
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62 ]]>
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63 </command>
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64 <version_string>sam-dump --version</version_string>
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65 <inputs>
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66 <expand macro="input_conditional"/>
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67 <param name="outputformat" type="select" label="select output format">
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68 <option value="bam">bam</option>
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69 <option value="sam">sam</option>
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70 </param>
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71 <param name="header" type="select" value="yes">
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72 <label>output header</label>
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73 <option value="yes">Yes</option>
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74 <option value="no">No</option>
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75 </param>
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76 <expand macro="alignments"/>
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77 <expand macro="region"/>
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78 <expand macro="matepairDist"/>
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79 <param name="primary" type="select" value="no">
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80 <label>only primary aligments</label>
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81 <option value="no">No</option>
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82 <option value="yes">Yes</option>
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83 </param>
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84 <expand macro="minMapq"></expand>
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85 </inputs>
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86 <outputs>
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87 <data name="output_accession" format="bam" label="${input.accession}.${outputformat}">
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88 <filter>input['input_select'] == "accession_number"</filter>
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89 <change_format>
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90 <when input="outputformat" value="sam" format="sam"/>
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91 </change_format>
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92 </data>
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93 <data name="output_file" format="bam" label="${input.file.name}.${outputformat}">
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94 <filter>input['input_select'] == "file"</filter>
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95 <change_format>
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96 <when input="outputformat" value="sam" format="sam"/>
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97 </change_format>
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98 </data>
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99 </outputs>
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100 <tests>
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101 <test>
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102 <param name="input_select" value="accession_number"/>
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103 <param name="accession" value="SRR925743"/>
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104 <param name="outputformat" value="sam"/>
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105 <param name="region" value="17:41243452-41277500"/>
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106 <output name="output_accession" file="sam_dump_result.sam" ftype="sam"/>
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107 </test>
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108 </tests>
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109 <help>
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110 This tool extracts reads from sra archives using sam-dump.
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111 The sam-dump program is developed at NCBI, and is available at
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112 http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software.
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113 @SRATOOLS_ATTRRIBUTION@
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114 </help>
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115 </tool>