Mercurial > repos > iuc > sra_tools
annotate sra_pileup.xml @ 15:f5ea3ce9b9b0 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
author | iuc |
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date | Tue, 10 Sep 2019 11:35:35 -0400 |
parents | c38286ea7047 |
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rev | line source |
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15
f5ea3ce9b9b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
iuc
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1 <tool id="sra_pileup" name="Download and Generate Pileup Format" version="@VERSION@.3"> |
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6c60903f70ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 6252dc2340b2fb6c7fdab2bdadfa4779c6f1aefd
iuc
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2 <description>from NCBI SRA</description> |
0
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
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3 <macros> |
b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
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4 <import>sra_macros.xml</import> |
b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
parents:
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5 </macros> |
b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
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6 <expand macro="requirements"/> |
b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
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7 <version_command>sra-pileup --version</version_command> |
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62e4d56ebb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 4091428e9e28ca06263bc00cdf938d20f620aa4d
iuc
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8 <command detect_errors="exit_code"> |
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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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9 <![CDATA[ |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1
iuc
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10 |
c7620aa7e1f0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1
iuc
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11 #if $input.input_select=="accession_number": |
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c38286ea7047
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 686710a7d313b828f1daed20c4055479727f2d91
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12 acc='${input.accession}' && [ ""\$acc" =~ ^[E|S|D]RR[0-9]{1,}$" ] && |
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c7620aa7e1f0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1
iuc
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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
iuc
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14 |
0
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
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15 ## Need to set the home directory to the current working directory, |
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f256cb398262
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 4e83a7f6d542cd3129eb14a142f74c127f91d026
iuc
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16 ## else the tool tries to write to home/.ncbi and fails when used |
f256cb398262
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 4e83a7f6d542cd3129eb14a142f74c127f91d026
iuc
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17 ## with a cluster manager. |
0
b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
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18 export HOME=\$PWD && |
b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
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19 vdb-config --restore-defaults && |
b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
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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
iuc
parents:
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21 #if ( str( $adv.region ) == "" ): |
b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
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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
iuc
parents:
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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
iuc
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24 prefetch -X 200G --ascp-path "\$ASCP_PATH|\$ASCP_KEY" "\$acc" && |
0
b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
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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
iuc
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26 ## sra-pileup command. |
b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
parents:
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27 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
iuc
parents:
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28 #end if |
b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
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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
iuc
parents:
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changeset
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30 #if str( $adv.region ) != "": |
b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
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31 --aligned-region "$adv.region" |
b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
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32 #end if |
b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
parents:
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33 #if str( $adv.minMapq ) != "": |
b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
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34 --minmapq "$adv.minMapq" |
b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
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35 #end if |
b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
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36 #if $input.input_select == "file": |
b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
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37 "$input.file" > "$output_file" |
b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
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38 #elif $input.input_select == "accession_number": |
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c7620aa7e1f0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1
iuc
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39 "\$acc" > "$output_accession" |
0
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
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40 #elif $input.input_select == "text": |
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c38286ea7047
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 686710a7d313b828f1daed20c4055479727f2d91
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41 `@ACCESSIONS_FROM_FILE@ '$input.text'` > "$output_text" |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
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42 #end if |
b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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43 ]]> |
b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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44 </command> |
b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
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45 <inputs> |
b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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46 <conditional name="input"> |
b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
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47 <param name="input_select" type="select" label="select input type"> |
b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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48 <option value="accession_number">SRR accession</option> |
b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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49 <option value="file">SRA archive in current history</option> |
b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
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50 <option value="text">text file containing SRR accession</option> |
b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
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51 </param> |
b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
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52 <when value="file"> |
b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
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53 <param format="sra" name="file" type="data" label="sra archive"/> |
b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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54 </when> |
b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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55 <when value="accession_number"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1
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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 <expand macro="sanitize_query" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1
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58 </param> |
0
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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59 </when> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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60 <when value="text"> |
b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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61 <param format="txt" name="text" type="data" label="text file"/> |
b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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62 </when> |
b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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63 </conditional> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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64 <section name="adv" title="Advanced Options" expanded="False"> |
b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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65 <expand macro="region"/> |
b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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66 <expand macro="minMapq"/> |
b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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67 </section> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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68 </inputs> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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69 <outputs> |
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70 <data format="pileup" name="output_accession" label="${input.accession} (sra-pileup)"> |
0
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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71 <filter>input['input_select'] == "accession_number"</filter> |
b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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72 </data> |
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73 <data format="pileup" name="output_file" label="${input.file.name} (sra-pileup)"> |
0
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
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74 <filter>input['input_select'] == "file"</filter> |
b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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75 </data> |
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76 <data format="pileup" name="output_text" label="${input.text.name} (sra-pileup)"> |
0
b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
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77 <filter>input['input_select'] == "text"</filter> |
b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
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78 </data> |
b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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79 </outputs> |
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80 <tests> |
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81 <test> |
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82 <param name="input_select" value="accession_number"/> |
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83 <param name="accession" value="SRR925743"/> |
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84 <param name="region" value="17:41243452-41277500"/> |
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85 <output name="output_accession" file="sra_pileup_result.pileup" compare="contains" ftype="pileup"/> |
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86 </test> |
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87 </tests> |
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88 <help> |
7
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89 <![CDATA[ |
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90 |
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91 This tool produces pileup format from sra archives using sra-pileup. |
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92 The sra-pileup program is developed at NCBI, and is available at |
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93 http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software. |
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94 @SRATOOLS_ATTRRIBUTION@ |
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95 |
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96 ]]> |
0
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97 </help> |
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98 <expand macro="citation"/> |
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99 </tool> |