Mercurial > repos > earlhaminst > blast_parser

annotate blast_parser.xml @ 4:363f3480622d draft default tip

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planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 598e396ffaf5834a1c8f32868b1568a2b48a0a78-dirty
author earlhaminst
date Thu, 12 Oct 2017 07:25:29 -0400
parents 70df762b48a8
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70df762b48a8 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 32272744ad83a704fd427b48aae574496a279901-dirty
earlhaminst
parents: 2
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1 <tool id="blast_parser" name="BLAST parser" version="0.1.2">
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87eda806422d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
earlhaminst
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2 <description>
87eda806422d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
earlhaminst
parents:
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3 Convert 12- or 24-column BLAST output into 3-column hcluster_sg input
87eda806422d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
earlhaminst
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4 </description>
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earlhaminst
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5 <command detect_errors="exit_code">
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87eda806422d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
earlhaminst
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6 <![CDATA[
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70df762b48a8 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 32272744ad83a704fd427b48aae574496a279901-dirty
earlhaminst
parents: 2
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7 python '$__tool_directory__/blast_parser.py'
70df762b48a8 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 32272744ad83a704fd427b48aae574496a279901-dirty
earlhaminst
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8 -i '$input'
70df762b48a8 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 32272744ad83a704fd427b48aae574496a279901-dirty
earlhaminst
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9 -o '$output'
70df762b48a8 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 32272744ad83a704fd427b48aae574496a279901-dirty
earlhaminst
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10 #if $reciprocal
70df762b48a8 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 32272744ad83a704fd427b48aae574496a279901-dirty
earlhaminst
parents: 2
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11 -r
70df762b48a8 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 32272744ad83a704fd427b48aae574496a279901-dirty
earlhaminst
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12 #end if
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87eda806422d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
earlhaminst
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13 ]]>
87eda806422d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
earlhaminst
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14 </command>
87eda806422d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
earlhaminst
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87eda806422d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
earlhaminst
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16 <inputs>
87eda806422d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
earlhaminst
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17 <param name="input" type="data" format="tabular" label="Tabular data" help="BLAST 12 column tabular format data"/>
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70df762b48a8 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 32272744ad83a704fd427b48aae574496a279901-dirty
earlhaminst
parents: 2
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18 <param name="reciprocal" type="boolean" checked="false" label="Reciprocal results" help="returns only reciprocal results"/>
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87eda806422d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
earlhaminst
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19 </inputs>
87eda806422d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
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87eda806422d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
earlhaminst
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21 <outputs>
87eda806422d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
earlhaminst
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22 <data name="output" format="tabular" label="$tool.name on ${on_string}" />
87eda806422d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
earlhaminst
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23 </outputs>
87eda806422d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
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87eda806422d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
earlhaminst
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25 <tests>
87eda806422d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
earlhaminst
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26 <test>
87eda806422d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
earlhaminst
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27 <param name="input" ftype="tabular" value="input.tabular" />
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70df762b48a8 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 32272744ad83a704fd427b48aae574496a279901-dirty
earlhaminst
parents: 2
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28 <param name="reciprocal" value="false" />
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87eda806422d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
earlhaminst
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29 <output name="output" file="output.tabular" />
87eda806422d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
earlhaminst
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30 </test>
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70df762b48a8 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 32272744ad83a704fd427b48aae574496a279901-dirty
earlhaminst
parents: 2
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31 <test>
70df762b48a8 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 32272744ad83a704fd427b48aae574496a279901-dirty
earlhaminst
parents: 2
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32 <param name="input" ftype="tabular" value="input.tabular" />
70df762b48a8 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 32272744ad83a704fd427b48aae574496a279901-dirty
earlhaminst
parents: 2
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33 <param name="reciprocal" value="true" />
70df762b48a8 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 32272744ad83a704fd427b48aae574496a279901-dirty
earlhaminst
parents: 2
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34 <output name="output" file="output2.tabular" />
70df762b48a8 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 32272744ad83a704fd427b48aae574496a279901-dirty
earlhaminst
parents: 2
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35 </test>
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87eda806422d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
earlhaminst
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36 </tests>
87eda806422d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
earlhaminst
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37 <help>
87eda806422d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
earlhaminst
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38 <![CDATA[
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70df762b48a8 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 32272744ad83a704fd427b48aae574496a279901-dirty
earlhaminst
parents: 2
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39 Simple tool to convert a 12- or 24-column BLAST output into a 3-column format (qseqid, sseqid, round(-1 * log10(evalue)/2)) usable as input for the hcluster_sg tool.
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87eda806422d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
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40 ]]>
87eda806422d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
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41 </help>
87eda806422d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
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42 <citations>
87eda806422d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
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43 </citations>
87eda806422d planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
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44 </tool>