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annotate clodius.xml @ 0:8a435cbdfe3f draft

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planemo upload for repository https://github.com/scottx611x/clodius-galaxy commit 66732f35a84835a50b6d3863e35e25b7291b9304-dirty
author scottx611x
date Tue, 03 Oct 2017 13:44:15 -0400
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1 <?xml version='1.0' encoding='utf-8'?>
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2
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3 <tool id="clodius" name="clodius" version="0.0.1">
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4 <description>Clodius is a tool for breaking up large data sets into smaller tiles that can subsequently be displayed using an appropriate viewer.</description>
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5 <requirements>
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6 <requirement type="package" version="0.3.2">pybigwig</requirement>
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7 <requirement type="package" version="0.2.19">negspy</requirement>
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8 <requirement type="package" version="1.0.7">slugid</requirement>
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9 <requirement type="package" version="0.6.5">clodius</requirement>
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10 </requirements>
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11 <command>
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12 <![CDATA[
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13 clodius aggregate $file_type $input_file --assembly $genome_assembly
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14
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15 #if $output_filename:
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16 --output-file $output_filename
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17 #end if
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18
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19 #if $file_type == "bedpe":
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20 --chr1-col $chromosome_one_column
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21 --from1-col $from_one_column
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22 --to1-col $to_one_column
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23 --chr2-col $chromosome_two_column
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24 --from2-col $from_two_column
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25 --to2-col $to_two_column
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26 #end if
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27
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28 #if $file_type == "bedfile":
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29 --max-per-tile $max_per_tile
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30 --importance-column $importance_column
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31 #if $delimiter == "tab":
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32 --delimiter '\t'
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33 #end if
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34 #end if
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35
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36 #if $file_type == "bedgraph":
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37 #if $chromosome_column:
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38 --chromosome-col $chromosome_column
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39 #end if
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40
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41 #if $from_position_column:
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42 --from-pos-col $from_position_column
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43 #end if
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44
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45 #if $to_position_column:
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46 --to-pos-col $to_position_column
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47 #end if
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48
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49 #if $value_column:
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50 --value-col $value_column
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51 #end if
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52
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53 #if $has_header:
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54 --has-header
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55 #end if
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56
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57 #if $nan_value:
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58 --nan-value $nan_value
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59 #end if
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60 #end if
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61 ]]>
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62 </command>
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63 <inputs>
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64 <param
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65 name="chromosome_column"
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66 type="integer"
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67 label="The column number (1-based) which contains the chromosome name."
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68 optional="true"/>
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69 <param
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70 name="chromosome_one_column"
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71 type="integer"
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72 label="The column containing the first chromosome."
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73 optional="true"/>
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74 <param
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75 name="chromosome_two_column"
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76 type="integer"
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77 label="The column containing the second chromosome."
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78 optional="true"/>
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79 <param
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80 name="delimiter"
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81 type="text"
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82 optional="true"/>
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83 <param
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84 name="file_type"
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85 type="text"
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86 label="Filetype to be aggregated">
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87 <option value="bedpe">Bedpe-like file</option>
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88 <option value="bedfile">Gene Annotation File</option>
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89 <option value="bedgraph">BedGraph file</option>
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90 <option value="bigwig">BigWig File</option>
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91 </param>
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parents:
diff changeset
92 <param
8a435cbdfe3f planemo upload for repository https://github.com/scottx611x/clodius-galaxy commit 66732f35a84835a50b6d3863e35e25b7291b9304-dirty
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diff changeset
93 name="from_one_column"
8a435cbdfe3f planemo upload for repository https://github.com/scottx611x/clodius-galaxy commit 66732f35a84835a50b6d3863e35e25b7291b9304-dirty
scottx611x
parents:
diff changeset
94 type="integer"
8a435cbdfe3f planemo upload for repository https://github.com/scottx611x/clodius-galaxy commit 66732f35a84835a50b6d3863e35e25b7291b9304-dirty
scottx611x
parents:
diff changeset
95 label="The column containing the first start position."
8a435cbdfe3f planemo upload for repository https://github.com/scottx611x/clodius-galaxy commit 66732f35a84835a50b6d3863e35e25b7291b9304-dirty
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parents:
diff changeset
96 optional="true"/>
8a435cbdfe3f planemo upload for repository https://github.com/scottx611x/clodius-galaxy commit 66732f35a84835a50b6d3863e35e25b7291b9304-dirty
scottx611x
parents:
diff changeset
97 <param
8a435cbdfe3f planemo upload for repository https://github.com/scottx611x/clodius-galaxy commit 66732f35a84835a50b6d3863e35e25b7291b9304-dirty
scottx611x
parents:
diff changeset
98 name="from_two_column"
8a435cbdfe3f planemo upload for repository https://github.com/scottx611x/clodius-galaxy commit 66732f35a84835a50b6d3863e35e25b7291b9304-dirty
scottx611x
parents:
diff changeset
99 type="integer"
8a435cbdfe3f planemo upload for repository https://github.com/scottx611x/clodius-galaxy commit 66732f35a84835a50b6d3863e35e25b7291b9304-dirty
scottx611x
parents:
diff changeset
100 label="The column containing the second start position."
8a435cbdfe3f planemo upload for repository https://github.com/scottx611x/clodius-galaxy commit 66732f35a84835a50b6d3863e35e25b7291b9304-dirty
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diff changeset
101 optional="true"/>
8a435cbdfe3f planemo upload for repository https://github.com/scottx611x/clodius-galaxy commit 66732f35a84835a50b6d3863e35e25b7291b9304-dirty
scottx611x
parents:
diff changeset
102 <param
8a435cbdfe3f planemo upload for repository https://github.com/scottx611x/clodius-galaxy commit 66732f35a84835a50b6d3863e35e25b7291b9304-dirty
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diff changeset
103 name="from_position_column"
8a435cbdfe3f planemo upload for repository https://github.com/scottx611x/clodius-galaxy commit 66732f35a84835a50b6d3863e35e25b7291b9304-dirty
scottx611x
parents:
diff changeset
104 type="integer"
8a435cbdfe3f planemo upload for repository https://github.com/scottx611x/clodius-galaxy commit 66732f35a84835a50b6d3863e35e25b7291b9304-dirty
scottx611x
parents:
diff changeset
105 label="The column number (1-based) which contains the starting position."
8a435cbdfe3f planemo upload for repository https://github.com/scottx611x/clodius-galaxy commit 66732f35a84835a50b6d3863e35e25b7291b9304-dirty
scottx611x
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diff changeset
106 value="2"/>
8a435cbdfe3f planemo upload for repository https://github.com/scottx611x/clodius-galaxy commit 66732f35a84835a50b6d3863e35e25b7291b9304-dirty
scottx611x
parents:
diff changeset
107 <param
8a435cbdfe3f planemo upload for repository https://github.com/scottx611x/clodius-galaxy commit 66732f35a84835a50b6d3863e35e25b7291b9304-dirty
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diff changeset
108 name="genome_assembly"
8a435cbdfe3f planemo upload for repository https://github.com/scottx611x/clodius-galaxy commit 66732f35a84835a50b6d3863e35e25b7291b9304-dirty
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diff changeset
109 type="text"
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diff changeset
110 label="Genome Assembly"
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diff changeset
111 value="hg19"/>
8a435cbdfe3f planemo upload for repository https://github.com/scottx611x/clodius-galaxy commit 66732f35a84835a50b6d3863e35e25b7291b9304-dirty
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diff changeset
112 <param
8a435cbdfe3f planemo upload for repository https://github.com/scottx611x/clodius-galaxy commit 66732f35a84835a50b6d3863e35e25b7291b9304-dirty
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diff changeset
113 name="has_header"
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diff changeset
114 type="boolean"
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diff changeset
115 label="Does this file have a header that we should ignore?"
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diff changeset
116 optional="true"/>
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diff changeset
117 <param
8a435cbdfe3f planemo upload for repository https://github.com/scottx611x/clodius-galaxy commit 66732f35a84835a50b6d3863e35e25b7291b9304-dirty
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diff changeset
118 name="input_file"
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diff changeset
119 type="data"
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diff changeset
120 label="File to be aggregated"/>
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diff changeset
121 <param
8a435cbdfe3f planemo upload for repository https://github.com/scottx611x/clodius-galaxy commit 66732f35a84835a50b6d3863e35e25b7291b9304-dirty
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122 name="importance_column"
8a435cbdfe3f planemo upload for repository https://github.com/scottx611x/clodius-galaxy commit 66732f35a84835a50b6d3863e35e25b7291b9304-dirty
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diff changeset
123 type="integer"
8a435cbdfe3f planemo upload for repository https://github.com/scottx611x/clodius-galaxy commit 66732f35a84835a50b6d3863e35e25b7291b9304-dirty
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124 label="The column (1-based) containing information about how important that row is.
8a435cbdfe3f planemo upload for repository https://github.com/scottx611x/clodius-galaxy commit 66732f35a84835a50b6d3863e35e25b7291b9304-dirty
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125 If it's absent, then use the length of the region.
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126 If the value is equal to `random`, then a random value will be used for the importance (effectively leading to random sampling)"
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diff changeset
127 optional="true"/>
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diff changeset
128 <param
8a435cbdfe3f planemo upload for repository https://github.com/scottx611x/clodius-galaxy commit 66732f35a84835a50b6d3863e35e25b7291b9304-dirty
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129 name="max_per_tile"
8a435cbdfe3f planemo upload for repository https://github.com/scottx611x/clodius-galaxy commit 66732f35a84835a50b6d3863e35e25b7291b9304-dirty
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diff changeset
130 type="integer"
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131 label="Max per tile."
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132 value="100"/>
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diff changeset
133 <param
8a435cbdfe3f planemo upload for repository https://github.com/scottx611x/clodius-galaxy commit 66732f35a84835a50b6d3863e35e25b7291b9304-dirty
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diff changeset
134 name="nan_value"
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diff changeset
135 type="text"
8a435cbdfe3f planemo upload for repository https://github.com/scottx611x/clodius-galaxy commit 66732f35a84835a50b6d3863e35e25b7291b9304-dirty
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136 label="The string to use as a NaN value."
8a435cbdfe3f planemo upload for repository https://github.com/scottx611x/clodius-galaxy commit 66732f35a84835a50b6d3863e35e25b7291b9304-dirty
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diff changeset
137 optional="true"/>
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diff changeset
138 <param
8a435cbdfe3f planemo upload for repository https://github.com/scottx611x/clodius-galaxy commit 66732f35a84835a50b6d3863e35e25b7291b9304-dirty
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139 name="output_filename"
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diff changeset
140 type="text"
8a435cbdfe3f planemo upload for repository https://github.com/scottx611x/clodius-galaxy commit 66732f35a84835a50b6d3863e35e25b7291b9304-dirty
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141 label="The default output file name to use. If this isn't specified, clodius will replace the current extension with something resonable."
8a435cbdfe3f planemo upload for repository https://github.com/scottx611x/clodius-galaxy commit 66732f35a84835a50b6d3863e35e25b7291b9304-dirty
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diff changeset
142 optional="true"/>
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diff changeset
143 <param
8a435cbdfe3f planemo upload for repository https://github.com/scottx611x/clodius-galaxy commit 66732f35a84835a50b6d3863e35e25b7291b9304-dirty
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diff changeset
144 name="to_one_column"
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diff changeset
145 type="integer"
8a435cbdfe3f planemo upload for repository https://github.com/scottx611x/clodius-galaxy commit 66732f35a84835a50b6d3863e35e25b7291b9304-dirty
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146 label="The column containing the first end position."
8a435cbdfe3f planemo upload for repository https://github.com/scottx611x/clodius-galaxy commit 66732f35a84835a50b6d3863e35e25b7291b9304-dirty
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diff changeset
147 optional="true"/>
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diff changeset
148 <param
8a435cbdfe3f planemo upload for repository https://github.com/scottx611x/clodius-galaxy commit 66732f35a84835a50b6d3863e35e25b7291b9304-dirty
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diff changeset
149 name="to_two_column"
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diff changeset
150 type="integer"
8a435cbdfe3f planemo upload for repository https://github.com/scottx611x/clodius-galaxy commit 66732f35a84835a50b6d3863e35e25b7291b9304-dirty
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diff changeset
151 label="The column containing the second end position."
8a435cbdfe3f planemo upload for repository https://github.com/scottx611x/clodius-galaxy commit 66732f35a84835a50b6d3863e35e25b7291b9304-dirty
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diff changeset
152 optional="true"/>
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diff changeset
153 <param
8a435cbdfe3f planemo upload for repository https://github.com/scottx611x/clodius-galaxy commit 66732f35a84835a50b6d3863e35e25b7291b9304-dirty
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154 name="to_position_column"
8a435cbdfe3f planemo upload for repository https://github.com/scottx611x/clodius-galaxy commit 66732f35a84835a50b6d3863e35e25b7291b9304-dirty
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diff changeset
155 type="integer"
8a435cbdfe3f planemo upload for repository https://github.com/scottx611x/clodius-galaxy commit 66732f35a84835a50b6d3863e35e25b7291b9304-dirty
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156 label="The column number (1-based) which contains the ending position."
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157 value="3"/>
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diff changeset
158 <param
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159 name="value_column"
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diff changeset
160 type="integer"
8a435cbdfe3f planemo upload for repository https://github.com/scottx611x/clodius-galaxy commit 66732f35a84835a50b6d3863e35e25b7291b9304-dirty
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161 label="The column number (1-based) which contains the actual value position."
8a435cbdfe3f planemo upload for repository https://github.com/scottx611x/clodius-galaxy commit 66732f35a84835a50b6d3863e35e25b7291b9304-dirty
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162 value="4"/>
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163 </inputs>
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164 <outputs>
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165 <data name="output_file" />
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diff changeset
166 </outputs>
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167 <tests>
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168 <test expect_num_outputs="1" expect_exit_code="0">
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169 <param name="input_file" value="Rao_RepA_GM12878_Arrowhead.txt"/>
8a435cbdfe3f planemo upload for repository https://github.com/scottx611x/clodius-galaxy commit 66732f35a84835a50b6d3863e35e25b7291b9304-dirty
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170 <param name="file_type" value="bedpe" />
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171 <param name="chromosome_one_column" value="1" />
8a435cbdfe3f planemo upload for repository https://github.com/scottx611x/clodius-galaxy commit 66732f35a84835a50b6d3863e35e25b7291b9304-dirty
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172 <param name="chromosome_two_column" value="1" />
8a435cbdfe3f planemo upload for repository https://github.com/scottx611x/clodius-galaxy commit 66732f35a84835a50b6d3863e35e25b7291b9304-dirty
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173 <param name="from_one_column" value="2" />
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174 <param name="from_two_column" value="2" />
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175 <param name="to_one_column" value="3" />
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176 <param name="to_two_column" value="3" />
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177 <param name="output_filename" value="bedpe_test.out" />
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178 <output name="output_file" file="Rao_RepA_GM12878_Arrowhead.txt.multires" />
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179 </test>
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180 <test expect_num_outputs="1" expect_exit_code="0">
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181 <param name="input_file" value="geneAnnotationsExonsUnions.short.bed" />
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182 <param name="file_type" value="bedfile" />
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183 <param name="importance_column" value="5" />
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184 <param name="max_per_tile" value="20" />
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185 <param name="output_filename" value="bedfile_test.out" />
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186 </test>
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187 <test expect_num_outputs="1" expect_exit_code="0">
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188 <param name="input_file" value="cnvs_hw.tsv" />
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189 <param name="file_type" value="bedgraph" />
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190 <param name="genome_assembly" value="grch37" />
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191 <param name="chromosome_column" value="2" />
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192 <param name="from_position_column" value="3" />
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193 <param name="to_position_column" value="4" />
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194 <param name="value_column" value="5" />
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195 <param name="has_header" value="true" />
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196 <param name="nan_value" value="NA" />
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197 <param name="output_filename" value="bedgraph_test.out" />
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198 </test>
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199 <test expect_num_outputs="1" expect_exit_code="0">
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200 <param name="input_file" value="test.bw" />
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201 <param name="file_type" value="bigwig" />
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202 <param name="output_filename" value="bigwig_test.out" />
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203 <output name="output_file" file="test.multires.bw" lines_diff="9"/>
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204 </test>
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205 </tests>
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206 <help>
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207 <![CDATA[
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208 **What it does**
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209 Clodius is a tool for breaking up large data sets into smaller tiles that can subsequently be displayed using an appropriate viewer.
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210 ]]>
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211 </help>
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212 </tool>