Mercurial > repos > iuc > crossmap_bw

annotate crossmap_bigwig.xml @ 2:fd6459edbad9 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
author iuc
date Thu, 19 Oct 2017 12:39:02 -0400
parents fb5401ff7ca2
children d3051afe9a38
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fb5401ff7ca2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
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1 <tool id="crossmap_bw" name="CrossMap BigWig" version="@WRAPPER_VERSION@-0">
fb5401ff7ca2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
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2 <description>Convert genome coordinates or annotation files between genome assemblies</description>
fb5401ff7ca2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
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3 <macros>
fb5401ff7ca2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
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4 <import>macros.xml</import>
fb5401ff7ca2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
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5 </macros>
fb5401ff7ca2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
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6 <expand macro="requirements"/>
fb5401ff7ca2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
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7 <expand macro="stdio"/>
fb5401ff7ca2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
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8 <expand macro="version_command"/>
fb5401ff7ca2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
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fb5401ff7ca2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
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10 <command><![CDATA[
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11 CrossMap.py bigwig
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12 '${chain_source.input_chain}'
fd6459edbad9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
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13 '${input}'
fd6459edbad9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
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14 '${output}'
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fb5401ff7ca2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
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15
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16 && mv '${output}.bw' '${output}'
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fb5401ff7ca2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
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17 ]]></command>
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19 <inputs>
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20 <param name="input" type="data" format="bigwig" label="BigWig file"/>
fd6459edbad9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
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21
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22 <expand macro="chain" />
fb5401ff7ca2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
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23 </inputs>
fb5401ff7ca2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
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25 <outputs>
2
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26 <data name="output" format="bigwig" label="${tool.name} on ${on_string}" />
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fb5401ff7ca2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
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27 </outputs>
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fb5401ff7ca2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
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29 <tests>
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30 <test>
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fd6459edbad9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
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31 <param name="input" value="test_bigwig_01_input_a.bw" ftype="bigwig"/>
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fb5401ff7ca2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
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32 <param name="index_source" value="history"/>
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fd6459edbad9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
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33 <param name="input_chain" value="aToB.over.chain" ftype="csv"/>
fd6459edbad9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
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fd6459edbad9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
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35 <output name="output" file="test_bigwig_01_output_a.bw"/>
fd6459edbad9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
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36 </test>
fd6459edbad9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
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37 <test><!-- cached chain file -->
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fb5401ff7ca2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
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38 <param name="input" value="test_bigwig_01_input_a.bw" ftype="bigwig"/>
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39 <param name="index_source" value="cached"/>
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fb5401ff7ca2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
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fb5401ff7ca2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
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41 <output name="output" file="test_bigwig_01_output_a.bw"/>
fb5401ff7ca2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
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42 </test>
fb5401ff7ca2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
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43 </tests>
fb5401ff7ca2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
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44 <help><![CDATA[
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45 @HELP_GENERAL@
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fb5401ff7ca2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
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47 BigWig
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48 ------
fb5401ff7ca2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
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49
2
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50 Input wiggle data can be in variableStep (for data with irregular
fd6459edbad9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
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51 intervals) or fixedStep (for data with regular intervals). Regardless of
fd6459edbad9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
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52 the input, the output will always in bedGraph format. bedGraph format is
fd6459edbad9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
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53 similar to wiggle format and can be converted into BigWig format using UCSC
fd6459edbad9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
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54 wigToBigWig tool. We export files in bedGraph because it is usually much
fd6459edbad9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
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55 smaller than file in wiggle format, and more importantly, CrossMap
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56 internally transforms wiggle into bedGraph to increase running speed.
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57
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58 ]]></help>
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60 <citations>
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61 <citation type="doi">10.1093/bioinformatics/btt730</citation>
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62 </citations>
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63 </tool>