Mercurial > repos > iuc > tn93_readreduce
annotate readreduce.xml @ 3:c176164dc8a5 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit e9f254ea1c6712a96512cae4df91bfec8207a492
| author | iuc |
|---|---|
| date | Sat, 28 Sep 2024 16:34:19 +0000 |
| parents | 1d2ec0b0a0a7 |
| children |
| rev | line source |
|---|---|
|
3
c176164dc8a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit e9f254ea1c6712a96512cae4df91bfec8207a492
iuc
parents:
2
diff
changeset
|
1 <tool id="tn93_readreduce" name="Merge matching reads" version="@TOOL_VERSION@+galaxy0"> |
|
0
bdaadfd0c843
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit 53d8d20f3b6716d7ce8d0f56916563d21fe3aa4a
iuc
parents:
diff
changeset
|
2 <description>into clusters with TN-93</description> |
|
bdaadfd0c843
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit 53d8d20f3b6716d7ce8d0f56916563d21fe3aa4a
iuc
parents:
diff
changeset
|
3 <macros> |
|
bdaadfd0c843
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit 53d8d20f3b6716d7ce8d0f56916563d21fe3aa4a
iuc
parents:
diff
changeset
|
4 <import>macros.xml</import> |
|
bdaadfd0c843
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit 53d8d20f3b6716d7ce8d0f56916563d21fe3aa4a
iuc
parents:
diff
changeset
|
5 </macros> |
|
2
1d2ec0b0a0a7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents:
0
diff
changeset
|
6 <expand macro="requirements" /> |
|
0
bdaadfd0c843
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit 53d8d20f3b6716d7ce8d0f56916563d21fe3aa4a
iuc
parents:
diff
changeset
|
7 <version_command><![CDATA[tn93 --version]]></version_command> |
|
bdaadfd0c843
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit 53d8d20f3b6716d7ce8d0f56916563d21fe3aa4a
iuc
parents:
diff
changeset
|
8 <command detect_errors="exit_code"><![CDATA[ |
|
bdaadfd0c843
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit 53d8d20f3b6716d7ce8d0f56916563d21fe3aa4a
iuc
parents:
diff
changeset
|
9 readreduce |
|
bdaadfd0c843
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit 53d8d20f3b6716d7ce8d0f56916563d21fe3aa4a
iuc
parents:
diff
changeset
|
10 -q |
|
bdaadfd0c843
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit 53d8d20f3b6716d7ce8d0f56916563d21fe3aa4a
iuc
parents:
diff
changeset
|
11 -o '$output' |
|
bdaadfd0c843
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit 53d8d20f3b6716d7ce8d0f56916563d21fe3aa4a
iuc
parents:
diff
changeset
|
12 #if str($options.advanced) == 'advanced': |
|
bdaadfd0c843
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit 53d8d20f3b6716d7ce8d0f56916563d21fe3aa4a
iuc
parents:
diff
changeset
|
13 -a $options.ambigs |
|
bdaadfd0c843
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit 53d8d20f3b6716d7ce8d0f56916563d21fe3aa4a
iuc
parents:
diff
changeset
|
14 -l $options.overlap |
|
bdaadfd0c843
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit 53d8d20f3b6716d7ce8d0f56916563d21fe3aa4a
iuc
parents:
diff
changeset
|
15 #if $options.counts_in_name: |
|
bdaadfd0c843
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit 53d8d20f3b6716d7ce8d0f56916563d21fe3aa4a
iuc
parents:
diff
changeset
|
16 -d '$options.counts_in_name' |
|
bdaadfd0c843
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit 53d8d20f3b6716d7ce8d0f56916563d21fe3aa4a
iuc
parents:
diff
changeset
|
17 #end if |
|
bdaadfd0c843
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit 53d8d20f3b6716d7ce8d0f56916563d21fe3aa4a
iuc
parents:
diff
changeset
|
18 -s '$size' |
|
bdaadfd0c843
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit 53d8d20f3b6716d7ce8d0f56916563d21fe3aa4a
iuc
parents:
diff
changeset
|
19 #end if |
|
bdaadfd0c843
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit 53d8d20f3b6716d7ce8d0f56916563d21fe3aa4a
iuc
parents:
diff
changeset
|
20 '$input' |
|
bdaadfd0c843
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit 53d8d20f3b6716d7ce8d0f56916563d21fe3aa4a
iuc
parents:
diff
changeset
|
21 ]]></command> |
|
bdaadfd0c843
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit 53d8d20f3b6716d7ce8d0f56916563d21fe3aa4a
iuc
parents:
diff
changeset
|
22 <inputs> |
|
bdaadfd0c843
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit 53d8d20f3b6716d7ce8d0f56916563d21fe3aa4a
iuc
parents:
diff
changeset
|
23 <param name="input" type="data" format="fasta" label="Input in FASTA format" /> |
|
bdaadfd0c843
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit 53d8d20f3b6716d7ce8d0f56916563d21fe3aa4a
iuc
parents:
diff
changeset
|
24 <conditional name="options"> |
|
bdaadfd0c843
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit 53d8d20f3b6716d7ce8d0f56916563d21fe3aa4a
iuc
parents:
diff
changeset
|
25 <param label="Additional options" name="advanced" type="select"> |
|
bdaadfd0c843
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit 53d8d20f3b6716d7ce8d0f56916563d21fe3aa4a
iuc
parents:
diff
changeset
|
26 <option value="defaults">Use defaults</option> |
|
bdaadfd0c843
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit 53d8d20f3b6716d7ce8d0f56916563d21fe3aa4a
iuc
parents:
diff
changeset
|
27 <option value="advanced">Specify additional parameters</option> |
|
bdaadfd0c843
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit 53d8d20f3b6716d7ce8d0f56916563d21fe3aa4a
iuc
parents:
diff
changeset
|
28 </param> |
|
bdaadfd0c843
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit 53d8d20f3b6716d7ce8d0f56916563d21fe3aa4a
iuc
parents:
diff
changeset
|
29 <when value="defaults" /> |
|
bdaadfd0c843
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit 53d8d20f3b6716d7ce8d0f56916563d21fe3aa4a
iuc
parents:
diff
changeset
|
30 <when value="advanced"> |
|
bdaadfd0c843
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit 53d8d20f3b6716d7ce8d0f56916563d21fe3aa4a
iuc
parents:
diff
changeset
|
31 <param name="size" argument="-s" type="integer" min="0" value="18" label="Mimimum cluster size to report in output" /> |
|
bdaadfd0c843
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit 53d8d20f3b6716d7ce8d0f56916563d21fe3aa4a
iuc
parents:
diff
changeset
|
32 <param name="ambigs" argument="-a" type="select" label="Strategy for ambiguous nucleotides"> |
|
bdaadfd0c843
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit 53d8d20f3b6716d7ce8d0f56916563d21fe3aa4a
iuc
parents:
diff
changeset
|
33 <option value="handle">handle</option> |
|
bdaadfd0c843
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit 53d8d20f3b6716d7ce8d0f56916563d21fe3aa4a
iuc
parents:
diff
changeset
|
34 <option value="resolve">resolve</option> |
|
bdaadfd0c843
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit 53d8d20f3b6716d7ce8d0f56916563d21fe3aa4a
iuc
parents:
diff
changeset
|
35 <option value="average">average</option> |
|
bdaadfd0c843
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit 53d8d20f3b6716d7ce8d0f56916563d21fe3aa4a
iuc
parents:
diff
changeset
|
36 <option value="skip">skip</option> |
|
bdaadfd0c843
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit 53d8d20f3b6716d7ce8d0f56916563d21fe3aa4a
iuc
parents:
diff
changeset
|
37 <option value="gapmm">gapmm</option> |
|
bdaadfd0c843
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit 53d8d20f3b6716d7ce8d0f56916563d21fe3aa4a
iuc
parents:
diff
changeset
|
38 </param> |
|
bdaadfd0c843
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit 53d8d20f3b6716d7ce8d0f56916563d21fe3aa4a
iuc
parents:
diff
changeset
|
39 <param name="overlap" argument="-l" type="integer" value="100" |
|
bdaadfd0c843
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit 53d8d20f3b6716d7ce8d0f56916563d21fe3aa4a
iuc
parents:
diff
changeset
|
40 label="Only count pairs that overlap by at least N bases" /> |
|
bdaadfd0c843
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit 53d8d20f3b6716d7ce8d0f56916563d21fe3aa4a
iuc
parents:
diff
changeset
|
41 <param name="counts_in_name" argument="-d" type="text" |
|
bdaadfd0c843
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit 53d8d20f3b6716d7ce8d0f56916563d21fe3aa4a
iuc
parents:
diff
changeset
|
42 optional="true" label="Sequence name component immediately preceding a copy number" /> |
|
bdaadfd0c843
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit 53d8d20f3b6716d7ce8d0f56916563d21fe3aa4a
iuc
parents:
diff
changeset
|
43 </when> |
|
bdaadfd0c843
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit 53d8d20f3b6716d7ce8d0f56916563d21fe3aa4a
iuc
parents:
diff
changeset
|
44 </conditional> |
|
bdaadfd0c843
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit 53d8d20f3b6716d7ce8d0f56916563d21fe3aa4a
iuc
parents:
diff
changeset
|
45 </inputs> |
|
bdaadfd0c843
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit 53d8d20f3b6716d7ce8d0f56916563d21fe3aa4a
iuc
parents:
diff
changeset
|
46 <outputs> |
|
bdaadfd0c843
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit 53d8d20f3b6716d7ce8d0f56916563d21fe3aa4a
iuc
parents:
diff
changeset
|
47 <data format="fasta" name="output" /> |
|
bdaadfd0c843
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit 53d8d20f3b6716d7ce8d0f56916563d21fe3aa4a
iuc
parents:
diff
changeset
|
48 </outputs> |
|
bdaadfd0c843
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit 53d8d20f3b6716d7ce8d0f56916563d21fe3aa4a
iuc
parents:
diff
changeset
|
49 <tests> |
|
bdaadfd0c843
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit 53d8d20f3b6716d7ce8d0f56916563d21fe3aa4a
iuc
parents:
diff
changeset
|
50 <test> |
|
bdaadfd0c843
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit 53d8d20f3b6716d7ce8d0f56916563d21fe3aa4a
iuc
parents:
diff
changeset
|
51 <param name="input" value="readreduce-in1.fa" /> |
|
bdaadfd0c843
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit 53d8d20f3b6716d7ce8d0f56916563d21fe3aa4a
iuc
parents:
diff
changeset
|
52 <output file="readreduce-out1.fa" ftype="fasta" name="output" sort="True" /> |
|
bdaadfd0c843
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit 53d8d20f3b6716d7ce8d0f56916563d21fe3aa4a
iuc
parents:
diff
changeset
|
53 </test> |
|
bdaadfd0c843
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit 53d8d20f3b6716d7ce8d0f56916563d21fe3aa4a
iuc
parents:
diff
changeset
|
54 <test> |
|
bdaadfd0c843
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit 53d8d20f3b6716d7ce8d0f56916563d21fe3aa4a
iuc
parents:
diff
changeset
|
55 <param name="input" value="readreduce-in2.fa" /> |
|
bdaadfd0c843
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit 53d8d20f3b6716d7ce8d0f56916563d21fe3aa4a
iuc
parents:
diff
changeset
|
56 <output file="readreduce-out2.fa" ftype="fasta" name="output" sort="True" /> |
|
bdaadfd0c843
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit 53d8d20f3b6716d7ce8d0f56916563d21fe3aa4a
iuc
parents:
diff
changeset
|
57 </test> |
|
bdaadfd0c843
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit 53d8d20f3b6716d7ce8d0f56916563d21fe3aa4a
iuc
parents:
diff
changeset
|
58 </tests> |
|
bdaadfd0c843
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit 53d8d20f3b6716d7ce8d0f56916563d21fe3aa4a
iuc
parents:
diff
changeset
|
59 <help>< algorithm. |
|
bdaadfd0c843
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit 53d8d20f3b6716d7ce8d0f56916563d21fe3aa4a
iuc
parents:
diff
changeset
|
65 ]]></help> |
|
bdaadfd0c843
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit 53d8d20f3b6716d7ce8d0f56916563d21fe3aa4a
iuc
parents:
diff
changeset
|
66 <expand macro="citations" /> |
|
bdaadfd0c843
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit 53d8d20f3b6716d7ce8d0f56916563d21fe3aa4a
iuc
parents:
diff
changeset
|
67 </tool> |