[2] | 1 | <tool id="cat1" name="Concatenate queries">
|
---|
| 2 | <description>tail-to-head</description>
|
---|
| 3 | <command interpreter="python">
|
---|
| 4 | catWrapper.py
|
---|
| 5 | $out_file1
|
---|
| 6 | $input1
|
---|
| 7 | #for $q in $queries
|
---|
| 8 | ${q.input2}
|
---|
| 9 | #end for
|
---|
| 10 | </command>
|
---|
| 11 | <inputs>
|
---|
| 12 | <param name="input1" type="data" label="Concatenate Query"/>
|
---|
| 13 | <repeat name="queries" title="Query">
|
---|
| 14 | <param name="input2" type="data" label="Select" />
|
---|
| 15 | </repeat>
|
---|
| 16 | </inputs>
|
---|
| 17 | <outputs>
|
---|
| 18 | <data name="out_file1" format="input" metadata_source="input1"/>
|
---|
| 19 | </outputs>
|
---|
| 20 | <tests>
|
---|
| 21 | <test>
|
---|
| 22 | <param name="input1" value="1.bed"/>
|
---|
| 23 | <param name="input2" value="2.bed"/>
|
---|
| 24 | <output name="out_file1" file="cat_wrapper_out1.bed"/>
|
---|
| 25 | </test>
|
---|
| 26 | <!--TODO: if possible, enhance the underlying test code to handle this test
|
---|
| 27 | the problem is multiple params with the same name "input2"
|
---|
| 28 | <test>
|
---|
| 29 | <param name="input1" value="1.bed"/>
|
---|
| 30 | <param name="input2" value="2.bed"/>
|
---|
| 31 | <param name="input2" value="3.bed"/>
|
---|
| 32 | <output name="out_file1" file="cat_wrapper_out2.bed"/>
|
---|
| 33 | </test>
|
---|
| 34 | -->
|
---|
| 35 | </tests>
|
---|
| 36 | <help>
|
---|
| 37 |
|
---|
| 38 | .. class:: warningmark
|
---|
| 39 |
|
---|
| 40 | **WARNING:** Be careful not to concatenate queries of different kinds (e.g., sequences with intervals). This tool does not check if the queries being concatenated are in the same format.
|
---|
| 41 |
|
---|
| 42 | -----
|
---|
| 43 |
|
---|
| 44 | **What it does**
|
---|
| 45 |
|
---|
| 46 | Concatenates queries
|
---|
| 47 |
|
---|
| 48 | -----
|
---|
| 49 |
|
---|
| 50 | **Example**
|
---|
| 51 |
|
---|
| 52 | Concatenating Query::
|
---|
| 53 |
|
---|
| 54 | chrX 151087187 151087355 A 0 -
|
---|
| 55 | chrX 151572400 151572481 B 0 +
|
---|
| 56 |
|
---|
| 57 | with Query1::
|
---|
| 58 |
|
---|
| 59 | chr1 151242630 151242955 X 0 +
|
---|
| 60 | chr1 151271715 151271999 Y 0 +
|
---|
| 61 | chr1 151278832 151279227 Z 0 -
|
---|
| 62 |
|
---|
| 63 | and with Query2::
|
---|
| 64 |
|
---|
| 65 | chr2 100000030 200000955 P 0 +
|
---|
| 66 | chr2 100000015 200000999 Q 0 +
|
---|
| 67 |
|
---|
| 68 | will result in the following::
|
---|
| 69 |
|
---|
| 70 | chrX 151087187 151087355 A 0 -
|
---|
| 71 | chrX 151572400 151572481 B 0 +
|
---|
| 72 | chr1 151242630 151242955 X 0 +
|
---|
| 73 | chr1 151271715 151271999 Y 0 +
|
---|
| 74 | chr1 151278832 151279227 Z 0 -
|
---|
| 75 | chr2 100000030 200000955 P 0 +
|
---|
| 76 | chr2 100000015 200000999 Q 0 +
|
---|
| 77 |
|
---|
| 78 | </help>
|
---|
| 79 | </tool>
|
---|