Mercurial > repos > matt-shirley > sra_tools
annotate sra_pileup.xml @ 47:04cc8176e86f draft default tip
update to SRA toolkit 2.3.3-3
author | Matt Shirley <mdshw5@gmail.com> |
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date | Mon, 16 Sep 2013 20:27:28 -0400 |
parents | 88a13a2fd23f |
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47
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update to SRA toolkit 2.3.3-3
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1 <tool id="sra_pileup" name="Generate pileup format" version="1.1.1"> |
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2 <description> from NCBI sra.</description> |
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3 <command>sra-pileup --log-level fatal |
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4 #if str( $region ) != "": |
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5 --aligned-region $region |
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6 #end if |
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7 #if str( $minMapq ) != "": |
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8 --minmapq $minMapq |
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9 #end if |
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10 #if $input.input_select == "file": |
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11 $input.file |
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12 #elif $input.input_select == "accession_number": |
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13 $input.accession |
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14 #elif $input.input_select == "text": |
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15 `cat $input.text` |
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16 #end if |
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17 > $output</command> |
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18 <version_string>sra-pileup --version</version_string> |
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19 <inputs> |
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20 <conditional name="input"> |
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21 <param name="input_select" type="select" label="select input type"> |
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22 <option value="accession_number">SRR accession</option> |
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23 <option value="file">SRA archive in current history</option> |
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24 <option value="text">text file containing SRR accession</option> |
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25 </param> |
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26 <when value="file"> |
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27 <param format="sra" name="file" type="data" label="sra archive"/> |
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28 </when> |
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29 <when value="accession_number"> |
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30 <param format="text" name="accession" type="text" label="accession"/> |
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31 </when> |
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32 <when value="text"> |
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33 <param format="txt" name="text" type="data" label="text file"/> |
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34 </when> |
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35 </conditional> |
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36 <param format="text" name="region" type="text" label="aligned region"/> |
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37 <param format="text" name="minMapq" type="text" label="minimum mapping quality"/> |
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38 </inputs> |
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39 <outputs> |
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40 <data format="pileup" name="output"/> |
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41 </outputs> |
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42 <requirements> |
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43 <requirement type="package" version="2.3.3-3">sra_toolkit</requirement> |
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44 </requirements> |
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45 <help> |
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46 This tool produces pileup format from sra archives using sra-pileup. |
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47 Browse the NCBI SRA for SRR accessions at http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=studies. |
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48 The sra-pileup program is developed at NCBI, and is available at: http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software. |
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49 Contact Matt Shirley at mdshw5@gmail.com for support and bug reports. |
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50 </help> |
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51 </tool> |