Mercurial > repos > iuc > sra_tools

annotate sra_pileup.xml @ 9:6c60903f70ac draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 6252dc2340b2fb6c7fdab2bdadfa4779c6f1aefd
author iuc
date Wed, 12 Jul 2017 00:48:56 -0400
parents c7620aa7e1f0
children c38286ea7047
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9
6c60903f70ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 6252dc2340b2fb6c7fdab2bdadfa4779c6f1aefd
iuc
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1 <tool id="sra_pileup" name="Download and Generate Pileup Format" version="@VERSION@.2">
6c60903f70ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 6252dc2340b2fb6c7fdab2bdadfa4779c6f1aefd
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2 <description>from NCBI SRA</description>
0
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3 <macros>
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4 <import>sra_macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
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7 <version_command>sra-pileup --version</version_command>
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iuc
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8 <command detect_errors="exit_code">
0
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9 <![CDATA[
7
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c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1
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11 #if $input.input_select=="accession_number":
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1
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12 acc="${input.accession}" &&
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1
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13 #end if
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1
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14
0
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15 ## Need to set the home directory to the current working directory,
2
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16 ## else the tool tries to write to home/.ncbi and fails when used
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17 ## with a cluster manager.
0
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18 export HOME=\$PWD &&
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19 vdb-config --restore-defaults &&
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20 vdb-config -s "/repository/user/main/public/root=\$PWD" &&
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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21 #if ( str( $adv.region ) == "" ):
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22 ASCP_PATH=`command -v ascp` &&
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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23 ASCP_KEY=`dirname \$ASCP_PATH`/asperaweb_id_dsa.openssh || true &&
7
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1
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24 prefetch -X 200G --ascp-path "\$ASCP_PATH|\$ASCP_KEY" "\$acc" &&
0
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25 ## Duplicate vdb-config, in case settings changed between prefetch and
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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26 ## sra-pileup command.
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27 vdb-config -s "/repository/user/main/public/root=\$PWD" &&
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28 #end if
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29 sra-pileup --log-level fatal
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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30 #if str( $adv.region ) != "":
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31 --aligned-region "$adv.region"
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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32 #end if
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33 #if str( $adv.minMapq ) != "":
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34 --minmapq "$adv.minMapq"
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35 #end if
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36 #if $input.input_select == "file":
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37 "$input.file" > "$output_file"
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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38 #elif $input.input_select == "accession_number":
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39 "\$acc" > "$output_accession"
0
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40 #elif $input.input_select == "text":
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41 `cat "$input.text"` > "$output_text"
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42 #end if
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43 ]]>
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44 </command>
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45 <inputs>
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46 <conditional name="input">
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47 <param name="input_select" type="select" label="select input type">
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48 <option value="accession_number">SRR accession</option>
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49 <option value="file">SRA archive in current history</option>
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50 <option value="text">text file containing SRR accession</option>
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51 </param>
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52 <when value="file">
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53 <param format="sra" name="file" type="data" label="sra archive"/>
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54 </when>
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55 <when value="accession_number">
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56 <param format="text" name="accession" type="text" label="SRR accession" help="Must start with SRR, e.g. SRR925743">
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57 <sanitizer>
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58 <valid initial="string.printable">
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59 <remove value=" "/>
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60 </valid>
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61 <mapping initial="none">
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62 <add source=" " target=""/>
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63 </mapping>
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64 </sanitizer>
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65 </param>
0
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66 </when>
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67 <when value="text">
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68 <param format="txt" name="text" type="data" label="text file"/>
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69 </when>
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70 </conditional>
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71 <section name="adv" title="Advanced Options" expanded="False">
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72 <expand macro="region"/>
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73 <expand macro="minMapq"/>
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74 </section>
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75 </inputs>
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76 <outputs>
7
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77 <data format="pileup" name="output_accession" label="${input.accession} (sra-pileup)">
0
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78 <filter>input['input_select'] == "accession_number"</filter>
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79 </data>
7
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80 <data format="pileup" name="output_file" label="${input.file.name} (sra-pileup)">
0
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81 <filter>input['input_select'] == "file"</filter>
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82 </data>
7
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83 <data format="pileup" name="output_text" label="${input.text.name} (sra-pileup)">
0
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84 <filter>input['input_select'] == "text"</filter>
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85 </data>
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86 </outputs>
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87 <tests>
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88 <test>
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89 <param name="input_select" value="accession_number"/>
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90 <param name="accession" value="SRR925743"/>
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91 <param name="region" value="17:41243452-41277500"/>
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92 <output name="output_accession" file="sra_pileup_result.pileup" compare="contains" ftype="pileup"/>
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93 </test>
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94 </tests>
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95 <help>
7
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96 <![CDATA[
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97
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98 This tool produces pileup format from sra archives using sra-pileup.
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99 The sra-pileup program is developed at NCBI, and is available at
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100 http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software.
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101 @SRATOOLS_ATTRRIBUTION@
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102
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103 ]]>
0
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104 </help>
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105 <expand macro="citation"/>
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106 </tool>