Mercurial > repos > iuc > maf_stats

annotate maf_stats.xml @ 1:0c84cce7b030 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ commit 95632be9aca24769ac192f2eb6a0454af21eff9e"
author iuc
date Tue, 10 Nov 2020 18:48:52 +0000
parents 5a92f4c476b5
children 87c1c223c704
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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1
0c84cce7b030 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ commit 95632be9aca24769ac192f2eb6a0454af21eff9e"
iuc
parents: 0
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1 <tool id="maf_stats1" name="MAF Coverage Stats" version="1.0.1+galaxy0">
0
5a92f4c476b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ commit f7b04f8c6edca90b1e9bc867a1569996aec76d7a"
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2 <description>Alignment coverage information</description>
5a92f4c476b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ commit f7b04f8c6edca90b1e9bc867a1569996aec76d7a"
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3 <command>
5a92f4c476b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ commit f7b04f8c6edca90b1e9bc867a1569996aec76d7a"
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4 <![CDATA[
5a92f4c476b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ commit f7b04f8c6edca90b1e9bc867a1569996aec76d7a"
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5 #if $maf_source_type.maf_source == 'cached'
5a92f4c476b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ commit f7b04f8c6edca90b1e9bc867a1569996aec76d7a"
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6 #set $tab = '\t'
5a92f4c476b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ commit f7b04f8c6edca90b1e9bc867a1569996aec76d7a"
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7 echo '$maf_source_type.mafType.fields.name${tab}$maf_source_type.mafType.fields.value${tab}$maf_source_type.mafType.fields.indexed_for${tab}$maf_source_type.mafType.fields.exists_in_maf${tab}$maf_source_type.mafType.fields.path' >> ./maf_index.loc &&
5a92f4c476b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ commit f7b04f8c6edca90b1e9bc867a1569996aec76d7a"
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8 #end if
5a92f4c476b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ commit f7b04f8c6edca90b1e9bc867a1569996aec76d7a"
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9 python '$__tool_directory__/maf_stats.py' $maf_source_type.maf_source
5a92f4c476b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ commit f7b04f8c6edca90b1e9bc867a1569996aec76d7a"
iuc
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10 #if $maf_source_type.maf_source == 'user':
5a92f4c476b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ commit f7b04f8c6edca90b1e9bc867a1569996aec76d7a"
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11 '$input2'
5a92f4c476b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ commit f7b04f8c6edca90b1e9bc867a1569996aec76d7a"
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12 #else:
5a92f4c476b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ commit f7b04f8c6edca90b1e9bc867a1569996aec76d7a"
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13 $maf_source_type.mafType.fields.value
5a92f4c476b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ commit f7b04f8c6edca90b1e9bc867a1569996aec76d7a"
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14 #end if
5a92f4c476b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ commit f7b04f8c6edca90b1e9bc867a1569996aec76d7a"
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15 '$input1' '$out_file1' $dbkey ${input1.metadata.chromCol} ${input1.metadata.startCol} ${input1.metadata.endCol} $summary '.'
5a92f4c476b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ commit f7b04f8c6edca90b1e9bc867a1569996aec76d7a"
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16 #if $maf_source_type.maf_source == 'user':
5a92f4c476b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ commit f7b04f8c6edca90b1e9bc867a1569996aec76d7a"
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17 '$input2.metadata.maf_index'
5a92f4c476b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ commit f7b04f8c6edca90b1e9bc867a1569996aec76d7a"
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18 #end if
5a92f4c476b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ commit f7b04f8c6edca90b1e9bc867a1569996aec76d7a"
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19 ]]>
5a92f4c476b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ commit f7b04f8c6edca90b1e9bc867a1569996aec76d7a"
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20 </command>
5a92f4c476b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ commit f7b04f8c6edca90b1e9bc867a1569996aec76d7a"
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21 <inputs>
5a92f4c476b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ commit f7b04f8c6edca90b1e9bc867a1569996aec76d7a"
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22 <param format="interval" name="input1" label="Interval File" type="data">
5a92f4c476b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ commit f7b04f8c6edca90b1e9bc867a1569996aec76d7a"
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23 <validator type="unspecified_build" />
5a92f4c476b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ commit f7b04f8c6edca90b1e9bc867a1569996aec76d7a"
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24 </param>
5a92f4c476b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ commit f7b04f8c6edca90b1e9bc867a1569996aec76d7a"
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25 <conditional name="maf_source_type">
5a92f4c476b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ commit f7b04f8c6edca90b1e9bc867a1569996aec76d7a"
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26 <param name="maf_source" type="select" label="MAF Source">
5a92f4c476b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ commit f7b04f8c6edca90b1e9bc867a1569996aec76d7a"
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27 <option value="cached" selected="true">Locally Cached Alignments</option>
5a92f4c476b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ commit f7b04f8c6edca90b1e9bc867a1569996aec76d7a"
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28 <option value="user">Alignments in Your History</option>
5a92f4c476b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ commit f7b04f8c6edca90b1e9bc867a1569996aec76d7a"
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29 </param>
5a92f4c476b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ commit f7b04f8c6edca90b1e9bc867a1569996aec76d7a"
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30 <when value="user">
5a92f4c476b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ commit f7b04f8c6edca90b1e9bc867a1569996aec76d7a"
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31 <param format="maf" name="input2" label="Choose alignments" type="data">
5a92f4c476b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ commit f7b04f8c6edca90b1e9bc867a1569996aec76d7a"
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32 <options>
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33 <filter type="data_meta" ref="input1" key="dbkey" />
5a92f4c476b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ commit f7b04f8c6edca90b1e9bc867a1569996aec76d7a"
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34 </options>
5a92f4c476b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ commit f7b04f8c6edca90b1e9bc867a1569996aec76d7a"
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35 <validator type="dataset_ok_validator" />
5a92f4c476b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ commit f7b04f8c6edca90b1e9bc867a1569996aec76d7a"
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36 </param>
5a92f4c476b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ commit f7b04f8c6edca90b1e9bc867a1569996aec76d7a"
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37 <param name="species" type="select" display="checkboxes" multiple="true" label="Choose species" help="Select species to be included in the final alignment">
5a92f4c476b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ commit f7b04f8c6edca90b1e9bc867a1569996aec76d7a"
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38 <options>
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39 <filter type="data_meta" ref="input2" key="species" />
5a92f4c476b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ commit f7b04f8c6edca90b1e9bc867a1569996aec76d7a"
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40 </options>
5a92f4c476b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ commit f7b04f8c6edca90b1e9bc867a1569996aec76d7a"
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41 </param>
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42 </when>
5a92f4c476b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ commit f7b04f8c6edca90b1e9bc867a1569996aec76d7a"
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43 <when value="cached">
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44 <param name="mafType" type="select" label="Choose alignments">
5a92f4c476b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ commit f7b04f8c6edca90b1e9bc867a1569996aec76d7a"
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45 <options from_data_table="maf_indexes">
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46 <column name="name" index="0"/>
5a92f4c476b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ commit f7b04f8c6edca90b1e9bc867a1569996aec76d7a"
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47 <column name="value" index="1"/>
5a92f4c476b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ commit f7b04f8c6edca90b1e9bc867a1569996aec76d7a"
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48 <column name="indexed_for" index="2"/>
5a92f4c476b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ commit f7b04f8c6edca90b1e9bc867a1569996aec76d7a"
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49 <column name="exists_in_maf" index="3" />
5a92f4c476b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ commit f7b04f8c6edca90b1e9bc867a1569996aec76d7a"
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50 <column name="path" index="4" />
5a92f4c476b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ commit f7b04f8c6edca90b1e9bc867a1569996aec76d7a"
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51 </options>
5a92f4c476b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ commit f7b04f8c6edca90b1e9bc867a1569996aec76d7a"
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52 </param>
5a92f4c476b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ commit f7b04f8c6edca90b1e9bc867a1569996aec76d7a"
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53 <param name="species" type="select" display="checkboxes" multiple="true" label="Choose species" help="Select species to be included in the final alignment">
5a92f4c476b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ commit f7b04f8c6edca90b1e9bc867a1569996aec76d7a"
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54 <options from_data_table="maf_indexes">
5a92f4c476b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ commit f7b04f8c6edca90b1e9bc867a1569996aec76d7a"
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55 <column name="value" index="3"/>
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56 <filter type="multiple_splitter" column="3" separator=","/>
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57 </options>
5a92f4c476b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ commit f7b04f8c6edca90b1e9bc867a1569996aec76d7a"
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58 </param>
5a92f4c476b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ commit f7b04f8c6edca90b1e9bc867a1569996aec76d7a"
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59 </when>
5a92f4c476b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ commit f7b04f8c6edca90b1e9bc867a1569996aec76d7a"
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60 </conditional>
5a92f4c476b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ commit f7b04f8c6edca90b1e9bc867a1569996aec76d7a"
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61 <param name="summary" type="select" label="Type of Output">
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62 <option value="false" selected="true">Coverage by Region</option>
5a92f4c476b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ commit f7b04f8c6edca90b1e9bc867a1569996aec76d7a"
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63 <option value="true">Summarize Coverage</option>
5a92f4c476b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ commit f7b04f8c6edca90b1e9bc867a1569996aec76d7a"
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64 </param>
5a92f4c476b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ commit f7b04f8c6edca90b1e9bc867a1569996aec76d7a"
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65 </inputs>
5a92f4c476b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ commit f7b04f8c6edca90b1e9bc867a1569996aec76d7a"
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66 <outputs>
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67 <data format="interval" name="out_file1" metadata_source="input1">
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68 <change_format>
5a92f4c476b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ commit f7b04f8c6edca90b1e9bc867a1569996aec76d7a"
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69 <when input="summary" value="true" format="tabular" />
5a92f4c476b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ commit f7b04f8c6edca90b1e9bc867a1569996aec76d7a"
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70 </change_format>
5a92f4c476b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ commit f7b04f8c6edca90b1e9bc867a1569996aec76d7a"
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71 </data>
5a92f4c476b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ commit f7b04f8c6edca90b1e9bc867a1569996aec76d7a"
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72 </outputs>
5a92f4c476b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ commit f7b04f8c6edca90b1e9bc867a1569996aec76d7a"
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73 <tests>
5a92f4c476b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ commit f7b04f8c6edca90b1e9bc867a1569996aec76d7a"
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74 <test>
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75 <param name="input1" value="maf_stats-in1.bed" dbkey="hg38" ftype="bed"/>
5a92f4c476b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ commit f7b04f8c6edca90b1e9bc867a1569996aec76d7a"
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76 <param name="maf_source" value="cached"/>
5a92f4c476b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ commit f7b04f8c6edca90b1e9bc867a1569996aec76d7a"
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77 <param name="mafType" value="TEST"/>
5a92f4c476b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ commit f7b04f8c6edca90b1e9bc867a1569996aec76d7a"
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78 <output name="out_file1" file="maf_stats-out1.dat"/>
5a92f4c476b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ commit f7b04f8c6edca90b1e9bc867a1569996aec76d7a"
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79 <param name="summary" value="false"/>
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80 </test>
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81 <test>
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82 <param name="input1" value="maf_stats-in2.bed" dbkey="hg38" ftype="bed"/>
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83 <param name="maf_source" value="cached"/>
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84 <param name="mafType" value="TEST"/>
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85 <output name="out_file1" file="maf_stats-out2.dat"/>
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86 <param name="summary" value="true"/>
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87 </test>
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88 </tests>
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89 <help>
5a92f4c476b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ commit f7b04f8c6edca90b1e9bc867a1569996aec76d7a"
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90 **What it does**
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91
5a92f4c476b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ commit f7b04f8c6edca90b1e9bc867a1569996aec76d7a"
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92 This tool takes a MAF file and an interval file and relates coverage information by interval for each species.
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93 If a column does not exist in the reference genome, it is not included in the output.
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94
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95 Consider the interval: "chrX 1000 1100 myInterval"
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96 Let's suppose we want to do stats on three way alignments for H, M, and R. The result look like this:
5a92f4c476b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ commit f7b04f8c6edca90b1e9bc867a1569996aec76d7a"
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97
5a92f4c476b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ commit f7b04f8c6edca90b1e9bc867a1569996aec76d7a"
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98 chrX 1000 1100 myInterval H XXX YYY
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99
5a92f4c476b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ commit f7b04f8c6edca90b1e9bc867a1569996aec76d7a"
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100 chrX 1000 1100 myInterval M XXX YYY
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101
5a92f4c476b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ commit f7b04f8c6edca90b1e9bc867a1569996aec76d7a"
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102 chrX 1000 1100 myInterval R XXX YYY
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103
5a92f4c476b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ commit f7b04f8c6edca90b1e9bc867a1569996aec76d7a"
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104
5a92f4c476b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ commit f7b04f8c6edca90b1e9bc867a1569996aec76d7a"
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105 where XXX and YYY are:
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106
5a92f4c476b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ commit f7b04f8c6edca90b1e9bc867a1569996aec76d7a"
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107 XXX = number of nucleotides
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108
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109 YYY = number of gaps
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110
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111 ----
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112
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113 Alternatively, you can request only summary information for a set of intervals:
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114
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115 ======== =========== ========
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116 #species nucleotides coverage
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117 ======== =========== ========
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118 hg18 30639 0.2372
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119 rheMac2 7524 0.0582
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120 panTro2 30390 0.2353
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121 ======== =========== ========
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122
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123 where **coverage** is the number of nucleotides divided by the total length of the provided intervals.
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124 </help>
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125 <citations>
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126 <citation type="doi">10.1093/bioinformatics/btr398</citation>
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127 </citations>
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128 </tool>