Mercurial > repos > iuc > sra_tools

annotate sra_pileup.xml @ 0:b723c120161a draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
author iuc
date Sun, 06 Dec 2015 09:04:37 -0500
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b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
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1 <tool id="sra_pileup" name="Generate pileup format" version="1.2.5">
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2 <description>from NCBI sra.</description>
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3 <macros>
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iuc
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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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8 <command>
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9 <![CDATA[
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10 ## Need to set the home directory to the current working directory,
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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11 ## else the tool tries to write to home/.ncbi and fails when used
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12 ## with a cluster manager.
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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13 export HOME=\$PWD &&
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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14 vdb-config --restore-defaults &&
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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15 vdb-config -s "/repository/user/main/public/root=\$PWD" &&
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16 #if ( str( $adv.region ) == "" ):
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17 ASCP_PATH=`command -v ascp` &&
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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18 ASCP_KEY=`dirname \$ASCP_PATH`/asperaweb_id_dsa.openssh || true &&
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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19 prefetch --ascp-path "\$ASCP_PATH|\$ASCP_KEY" "$input.accession" &&
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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20 ## 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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21 ## sra-pileup command.
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22 vdb-config -s "/repository/user/main/public/root=\$PWD" &&
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23 #end if
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24 sra-pileup --log-level fatal
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25 #if str( $adv.region ) != "":
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26 --aligned-region "$adv.region"
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27 #end if
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28 #if str( $adv.minMapq ) != "":
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29 --minmapq "$adv.minMapq"
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30 #end if
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31 #if $input.input_select == "file":
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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32 "$input.file" > "$output_file"
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33 #elif $input.input_select == "accession_number":
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34 "$input.accession" > "$output_accession"
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35 #elif $input.input_select == "text":
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36 `cat "$input.text"` > "$output_text"
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37 #end if
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38 ]]>
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39 </command>
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40 <inputs>
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41 <conditional name="input">
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42 <param name="input_select" type="select" label="select input type">
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43 <option value="accession_number">SRR accession</option>
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44 <option value="file">SRA archive in current history</option>
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45 <option value="text">text file containing SRR accession</option>
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46 </param>
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47 <when value="file">
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48 <param format="sra" name="file" type="data" label="sra archive"/>
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49 </when>
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50 <when value="accession_number">
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51 <param format="text" name="accession" type="text" label="SRR accession" help="Must start with SRR, e.g. SRR925743"/>
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52 </when>
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53 <when value="text">
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54 <param format="txt" name="text" type="data" label="text file"/>
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55 </when>
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56 </conditional>
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57 <section name="adv" title="Advanced Options" expanded="False">
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58 <expand macro="region"/>
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59 <expand macro="minMapq"/>
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60 </section>
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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" compare="contains" 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 <expand macro="citation"/>
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parents:
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88 </tool>