root/galaxy-central/tools/filters/joiner.xml

リビジョン 2, 7.3 KB (コミッタ: hatakeyama, 14 年 前)

import galaxy-central

行番号 
1<tool id="join1" name="Join two Queries" version="2.0.2">
2  <description>side by side on a specified field</description>
3  <command interpreter="python">join.py $input1 $input2 $field1 $field2 $out_file1 $unmatched $partial --index_depth=3 --buffer=50000000 --fill_options_file=$fill_options_file</command>
4  <inputs>
5    <param format="tabular" name="input1" type="data" label="Join"/>
6    <param name="field1" label="using column" type="data_column" data_ref="input1" />
7    <param format="tabular" name="input2" type="data" label="with" />
8    <param name="field2" label="and column" type="data_column" data_ref="input2" />
9    <param name="unmatched" type="select" label="Keep lines of first input that do not join with second input">
10      <option value="-u">Yes</option>
11      <option value="" selected="true">No</option>
12    </param>
13    <param name="partial" type="select" label="Keep lines of first input that are incomplete">
14      <option value="-p">Yes</option>
15      <option value="" selected="true">No</option>
16    </param>
17    <conditional name="fill_empty_columns">
18      <param name="fill_empty_columns_switch" type="select" label="Fill empty columns">
19        <option value="no_fill" selected="True">No</option>
20        <option value="fill_empty">Yes</option>
21      </param>
22     <when value="no_fill">
23        <!-- do nothing -->
24     </when>
25     <when value="fill_empty">
26       <param type="select" name="fill_columns_by" label="Only fill unjoined rows">
27         <option value="fill_unjoined_only" selected="True">Yes</option>
28         <option value="fill_all">No</option>
29       </param>
30       <conditional name="do_fill_empty_columns">
31         <param name="column_fill_type" type="select" label="Fill Columns by">
32           <option value="single_fill_value" selected="True">Single fill value</option>
33           <option value="fill_value_by_column">Values by column</option>
34         </param>
35         <when value="single_fill_value">
36           <param type="text" name="fill_value" label="Fill value" value="."/>
37         </when>
38         <when value="fill_value_by_column">
39           <repeat name="column_fill1" title="Fill Column for Input 1">
40             <param name="column_number1" label="Column" type="data_column" data_ref="input1" />
41             <param type="text" name="fill_value1" value="."/>
42           </repeat>
43           <repeat name="column_fill2" title="Fill Column for Input 2">
44             <param name="column_number2" label="Column" type="data_column" data_ref="input2" />
45             <param type="text" name="fill_value2" value="."/>
46           </repeat>
47         </when>
48       </conditional>
49     </when>
50   </conditional>
51  </inputs>
52  <configfiles>
53    <configfile name="fill_options_file">&lt;%
54import simplejson
55%&gt;
56#set $__fill_options = {}
57#if $fill_empty_columns['fill_empty_columns_switch'] == 'fill_empty':
58    #set $__fill_options['fill_unjoined_only'] = $fill_empty_columns['fill_columns_by'].value == 'fill_unjoined_only'
59    #if $fill_empty_columns['do_fill_empty_columns']['column_fill_type'] == 'single_fill_value':
60        #set $__start_fill = $fill_empty_columns['do_fill_empty_columns']['fill_value'].value
61    #else:
62        #set $__start_fill = ""
63    #end if
64    #set $__fill_options['file1_columns'] = [ __start_fill for i in range( int( $input1.metadata.columns ) ) ]
65    #set $__fill_options['file2_columns'] = [ __start_fill for i in range( int( $input2.metadata.columns ) ) ]
66    #if $fill_empty_columns['do_fill_empty_columns']['column_fill_type'] == 'fill_value_by_column':
67        #for column_fill1 in $fill_empty_columns['do_fill_empty_columns']['column_fill1']:
68            #set $__fill_options['file1_columns'][ int( column_fill1['column_number1'].value ) - 1 ] = column_fill1['fill_value1'].value
69        #end for
70        #for column_fill2 in $fill_empty_columns['do_fill_empty_columns']['column_fill2']:
71            #set $__fill_options['file2_columns'][ int( column_fill2['column_number2'].value ) - 1 ] = column_fill2['fill_value2'].value
72        #end for
73    #end if
74#end if
75${simplejson.dumps( __fill_options )}
76    </configfile>
77  </configfiles>
78  <outputs>
79     <data format="input" name="out_file1" metadata_source="input1" />
80  </outputs>
81  <tests>
82    <test>
83      <param name="input1" value="1.bed"/>
84      <param name="input2" value="2.bed"/>
85      <param name="field1" value="2"/>
86      <param name="field2" value="2"/>
87      <param name="unmatched" value=""/>
88      <param name="partial" value=""/>
89      <param name="fill_empty_columns_switch" value="no_fill"/>
90      <output name="out_file1" file="joiner_out1.bed"/>
91    </test>
92    <test>
93      <param name="input1" value="1.bed"/>
94      <param name="input2" value="2.bed"/>
95      <param name="field1" value="2"/>
96      <param name="field2" value="2"/>
97      <param name="unmatched" value="Yes"/>
98      <param name="partial" value="Yes"/>
99      <param name="fill_empty_columns_switch" value="no_fill"/>
100      <output name="out_file1" file="joiner_out2.bed"/>
101    </test>
102    <test>
103      <param name="input1" value="1.bed"/>
104      <param name="input2" value="2.bed"/>
105      <param name="field1" value="2"/>
106      <param name="field2" value="2"/>
107      <param name="unmatched" value="Yes"/>
108      <param name="partial" value="Yes"/>
109      <param name="fill_empty_columns_switch" value="fill_empty"/>
110      <param name="fill_columns_by" value="fill_all"/>
111      <param name="column_fill_type" value="single_fill_value"/>
112      <param name="fill_value" value="~"/>
113      <output name="out_file1" file="joiner_out3.bed"/>
114    </test>
115    <test>
116      <param name="input1" value="1.bed"/>
117      <param name="input2" value="2.bed"/>
118      <param name="field1" value="2"/>
119      <param name="field2" value="2"/>
120      <param name="unmatched" value="Yes"/>
121      <param name="partial" value="Yes"/>
122      <param name="fill_empty_columns_switch" value="fill_empty"/>
123      <param name="fill_columns_by" value="fill_all"/>
124      <param name="column_fill_type" value="fill_value_by_column"/>
125      <param name="column_number1" value="6"/>
126      <param name="fill_value1" value="+"/>
127      <param name="column_number2" value="1"/>
128      <param name="fill_value2" value="NoChrom"/>
129      <output name="out_file1" file="joiner_out4.bed"/>
130    </test>
131  </tests>
132  <help>
133
134.. class:: warningmark
135
136**This tool will attempt to reuse the metadata from your first input.** To change metadata assignments click on the "edit attributes" link of the history item generated by this tool.
137
138.. class:: infomark
139
140**TIP:** If your data is not TAB delimited, use *Text Manipulation-&gt;Convert*
141
142-----
143
144**Syntax**
145
146This tool joins lines of two queries on a common field. An empty string ("") is not a valid identifier.
147You may choose to include lines of your first input that do not join with your second input.
148
149- Columns are referenced with a **number**. For example, **3** refers to the 3rd column of a tab-delimited file.
150
151-----
152
153**Example**
154
155Query1::
156
157  chr1 10 20 geneA
158  chr1 50 80 geneB
159  chr5 10 40 geneL
160
161Query2::
162
163  geneA tumor-supressor
164  geneB Foxp2
165  geneC Gnas1
166  geneE INK4a
167
168Joining the 4th column of Query1 with the 1st column of Query2 will yield::
169
170  chr1 10 20 geneA geneA tumor-suppressor
171  chr1 50 80 geneB geneB Foxp2
172
173Joining the 4th column of Query1 with the 1st column of Query2, while keeping all lines from Query1, will yield::
174
175  chr1 10 20 geneA geneA tumor-suppressor
176  chr1 50 80 geneB geneB Foxp2
177  chr5 10 40 geneL
178
179</help>
180</tool>
Note: リポジトリブラウザについてのヘルプは TracBrowser を参照してください。