Mercurial > repos > iuc > stacks2_procrad
annotate stacks_procrad.xml @ 7:1f50934aed1d draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit feda4e2ea70c013fcddd1dbdeab73158fe9c86a4
| author | iuc |
|---|---|
| date | Mon, 23 May 2022 17:43:15 +0000 |
| parents | 02be7d7634b0 |
| children |
| rev | line source |
|---|---|
|
5
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
1 <tool id="stacks2_procrad" name="Stacks2: process radtags" profile="@PROFILE@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> |
|
0
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
2 <description>the Stacks demultiplexing script</description> |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
3 <macros> |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
4 <import>macros.xml</import> |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
5 <import>macros_process.xml</import> |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
6 </macros> |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
7 <expand macro="requirements"/> |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
8 <expand macro="version_cmd"/> |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
9 <command detect_errors="aggressive"><![CDATA[ |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
10 @FASTQ_INPUT_FUNCTIONS@ |
|
2
bdd7e518c7d0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents:
1
diff
changeset
|
11 |
|
5
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
12 #if $input_type.barcode_encoding != '' |
|
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
13 python '$__tool_directory__'/check_bcfile.py '$input_type.barcode' && |
|
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
14 #end if |
|
0
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
15 mkdir stacks_inputs stacks_outputs && |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
16 |
|
1
56f6477cf37b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit c300b84615660459bb0020fa74ccd3b874d329a4"
iuc
parents:
0
diff
changeset
|
17 #if $output_log |
|
56f6477cf37b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit c300b84615660459bb0020fa74ccd3b874d329a4"
iuc
parents:
0
diff
changeset
|
18 ln -s '$output_log' stacks_outputs/process_radtags.stacks_inputs.log && |
|
56f6477cf37b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit c300b84615660459bb0020fa74ccd3b874d329a4"
iuc
parents:
0
diff
changeset
|
19 #end if |
|
56f6477cf37b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit c300b84615660459bb0020fa74ccd3b874d329a4"
iuc
parents:
0
diff
changeset
|
20 |
|
0
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
21 #set ($link_command, $inputype) = $fastq_input_nonbatch( $input_type.fqinputs, $input_type.input_type_select, "_R%d_0" ) |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
22 $link_command |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
23 |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
24 process_radtags |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
25 |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
26 @PROCESS_IOOPTIONS@ |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
27 @PROCESS_FILTER@ |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
28 @COMMON_ADVANCED@ |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
29 @RESCUE_BARCODE@ |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
30 @PROCESS_ADAPTER@ |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
31 |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
32 ## -E not implemented in Galaxy defaults to phred33 |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
33 |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
34 ## Restriction enzyme options |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
35 #if str($options_enzyme.enzyme) != '': |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
36 -e $options_enzyme.enzyme |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
37 #end if |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
38 #if str( $options_enzyme.options_enzyme_selector ) == "2" and str($options_enzyme.enzyme2)!='': |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
39 --renz_2 $options_enzyme.enzyme2 |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
40 #end if |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
41 |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
42 ## advanced options not shared between shortreads and radtags |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
43 $options_advanced.bestrad |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
44 $options_advanced.disable_rad_check |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
45 |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
46 ## Output options |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
47 ## --merge not implemented in Galaxy |
|
1
56f6477cf37b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit c300b84615660459bb0020fa74ccd3b874d329a4"
iuc
parents:
0
diff
changeset
|
48 |
|
0
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
49 @PROCESS_FASTQ_POSTPROC@ |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
50 ]]></command> |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
51 |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
52 <inputs> |
|
5
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
53 <conditional name="input_type"> |
|
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
54 <param name="input_type_select" type="select" label="Single-end or paired-end reads"> |
|
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
55 <option value="single" selected="True">Single-end files</option> |
|
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
56 <option value="paired">Paired-end files</option> |
|
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
57 </param> |
|
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
58 <when value="single"> |
|
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
59 <param name="fqinputs" argument="-f" type="data" format="fastqsanger,fastqsanger.gz" multiple="true" label="Singles-end reads"/> |
|
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
60 <expand macro="barcode_selector"> |
|
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
61 <expand macro="barcode_encoding_single" type="Barcode"/> |
|
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
62 </expand> |
|
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
63 </when> |
|
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
64 <when value="paired"> |
|
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
65 <param name="fqinputs" type="data_collection" collection_type="list:paired" label="Paired-end reads" format="fastqsanger,fastqsanger.gz"/> |
|
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
66 <expand macro="barcode_selector"> |
|
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
67 <expand macro="barcode_encoding_pair" type="Barcode"/> |
|
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
68 </expand> |
|
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
69 </when> |
|
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
70 </conditional> |
|
0
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
71 <conditional name="options_enzyme"> |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
72 <param name="options_enzyme_selector" type="select" label="Number of enzymes"> |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
73 <option value="1">One</option> |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
74 <option value="2">Two</option> |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
75 </param> |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
76 <when value="1"> |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
77 <param name="enzyme" type="select" label="Enzyme" argument="-e" help="provide the restriction enzyme used" > |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
78 <expand macro="enzymes"/> |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
79 </param> |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
80 </when> |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
81 <when value="2"> |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
82 <param name="enzyme" type="select" label="Enzyme" argument="-e" help="provide the restriction enzyme used" > |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
83 <expand macro="enzymes"/> |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
84 </param> |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
85 <param name="enzyme2" type="select" label="Second enzyme" argument="--renz_2" help="provide the second restriction enzyme used" > |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
86 <expand macro="enzymes"/> |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
87 </param> |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
88 </when> |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
89 </conditional> |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
90 |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
91 <section name="options_advanced" title="advanced options" expanded="False"> |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
92 <expand macro="common_advanced"/> |
|
2
bdd7e518c7d0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents:
1
diff
changeset
|
93 <param argument="--bestrad" type="boolean" checked="false" truevalue="--bestrad" falsevalue="" label="Library was generated using BestRAD, check for restriction enzyme on either read and potentially tranpose reads"/> |
|
bdd7e518c7d0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents:
1
diff
changeset
|
94 <param argument="--disable_rad_check" type="boolean" checked="false" truevalue="--disable_rad_check" falsevalue="" label="Disable checking if the RAD site is intact"/> |
|
0
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
95 <expand macro="rescue_barcode"/> |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
96 <expand macro="process_adapter"/> |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
97 </section> |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
98 |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
99 <expand macro="process_filter"/> |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
100 <expand macro="process_output_types"/> |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
101 <expand macro="in_log"/> |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
102 </inputs> |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
103 |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
104 <outputs> |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
105 <expand macro="out_log"/> |
|
5
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
106 <expand macro="process_outputs"> |
|
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
107 <collection name="processed" type="list" label="${tool.name} on ${on_string} Processed reads"> |
|
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
108 <filter>input_type['input_type_select'] == "single"</filter> |
|
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
109 <filter>input_type['barcode_encoding'] == ""</filter> |
|
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
110 <expand macro="discover_faqgz_output_macro" pattern="(?P<name>.+)" dir="stacks_outputs"/> |
|
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
111 </collection> |
|
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
112 <collection name="processed_paired" type="list:paired" label="${tool.name} on ${on_string} Processed reads"> |
|
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
113 <filter>input_type['input_type_select'] == "paired"</filter> |
|
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
114 <filter>input_type['barcode_encoding'] == ""</filter> |
|
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
115 <expand macro="discover_faqgz_output_macro" pattern="(?P<identifier_0>.+)\.(?P<identifier_1>[^.]+)" dir="stacks_outputs"/> |
|
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
116 </collection> |
|
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
117 <collection name="demultiplexed" type="list" label="${tool.name} on ${on_string} Demultiplexed reads"> |
|
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
118 <filter>input_type['input_type_select'] == "single"</filter> |
|
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
119 <filter>input_type['barcode_encoding'] != ""</filter> |
|
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
120 <expand macro="discover_faqgz_output_macro" pattern="(?P<name>.+)" dir="stacks_outputs"/> |
|
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
121 </collection> |
|
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
122 <collection name="demultiplexed_paired" type="list:paired" label="${tool.name} on ${on_string} Demultiplexed reads"> |
|
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
123 <filter>input_type['input_type_select'] == "paired"</filter> |
|
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
124 <filter>input_type['barcode_encoding'] != ""</filter> |
|
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
125 <expand macro="discover_faqgz_output_macro" pattern="(?P<identifier_0>.+)\.(?P<identifier_1>[^.]+)" dir="stacks_outputs"/> |
|
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
126 </collection> |
|
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
127 </expand> |
|
0
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
128 </outputs> |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
129 <tests> |
|
5
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
130 <!-- 01 single single ended input, no filtering (hence no capturing) + log --> |
|
2
bdd7e518c7d0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents:
1
diff
changeset
|
131 <test expect_num_outputs="2"> |
|
0
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
132 <param name="input_type|input_type_select" value="single"/> |
|
5
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
133 <param name="input_type|fqinputs" ftype="fastqsanger" value="procrad/R1_01.fq,procrad/R1_02.fq,procrad/R1_03.fq,procrad/R1_04.fq"/> |
|
0
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
134 <param name="input_type|barcode_encoding" value="--inline_null"/> |
|
5
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
135 <param name="input_type|barcode" value="procrad/barcodes"/> |
|
0
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
136 <param name="options_enzyme|options_enzyme_selector" value="1"/> |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
137 <param name="options_enzyme|enzyme" value="ecoRI"/> |
|
2
bdd7e518c7d0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents:
1
diff
changeset
|
138 <param name="add_log" value="yes"/> |
|
0
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
139 <output name="output_log" file="procrad/process_radtags.out" lines_diff="4"/> |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
140 <output_collection name="demultiplexed" count="40"> |
|
5
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
141 <element name="PopA_01" file="demultiplexed/PopA_01.fq" ftype="fastqsanger" compare="contains"/> |
|
0
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
142 </output_collection> |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
143 </test> |
|
5
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
144 <!-- 02 multiple (zipped) single end input (misusing R2 as add single end read file), |
|
0
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
145 discarding by quality and capturing them --> |
|
2
bdd7e518c7d0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents:
1
diff
changeset
|
146 <test expect_num_outputs="3"> |
|
0
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
147 <param name="input_type|input_type_select" value="single"/> |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
148 <param name="input_type|fqinputs" ftype="fastqsanger.gz" value="procrad/R1.fq.gzip,procrad/R2.fq.gzip"/> |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
149 <param name="input_type|barcode_encoding" value="--inline_null"/> |
|
5
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
150 <param name="input_type|barcode" value="procrad/barcodes"/> |
|
0
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
151 <param name="options_enzyme|options_enzyme_selector" value="1"/> |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
152 <param name="options_enzyme|enzyme" value="ecoRI"/> |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
153 <param name="filter_cond|filter_select" value="yes"/> |
|
1
56f6477cf37b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit c300b84615660459bb0020fa74ccd3b874d329a4"
iuc
parents:
0
diff
changeset
|
154 <param name="filter_cond|discard" value="-q"/> |
|
2
bdd7e518c7d0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents:
1
diff
changeset
|
155 <param name="filter_cond|sliding" value="0.1"/> |
|
bdd7e518c7d0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents:
1
diff
changeset
|
156 <param name="filter_cond|score" value="11"/> |
|
bdd7e518c7d0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents:
1
diff
changeset
|
157 <param name="filter_cond|remove" value="-c"/> |
|
1
56f6477cf37b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit c300b84615660459bb0020fa74ccd3b874d329a4"
iuc
parents:
0
diff
changeset
|
158 <param name="capture" value="-D"/> |
|
0
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
159 <param name="outype" value="gzfastq"/> |
|
2
bdd7e518c7d0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents:
1
diff
changeset
|
160 <param name="add_log" value="yes"/> |
|
1
56f6477cf37b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit c300b84615660459bb0020fa74ccd3b874d329a4"
iuc
parents:
0
diff
changeset
|
161 <output name="output_log" file="procrad/process_radtags2.out" lines_diff="4"/> |
|
0
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
162 <assert_command> |
|
2
bdd7e518c7d0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents:
1
diff
changeset
|
163 <has_text text="-q"/> |
|
bdd7e518c7d0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents:
1
diff
changeset
|
164 <has_text text="-w 0.1"/> |
|
bdd7e518c7d0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents:
1
diff
changeset
|
165 <has_text text="-s 11"/> |
|
bdd7e518c7d0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents:
1
diff
changeset
|
166 <has_text text="-c"/> |
|
bdd7e518c7d0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents:
1
diff
changeset
|
167 <has_text text="-D"/> |
|
0
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
168 </assert_command> |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
169 <output_collection name="demultiplexed" count="40"> |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
170 <element name="PopA_01" ftype="fastqsanger.gz" md5="c7250f50138cbca747b85223aaae9565"/> |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
171 </output_collection> |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
172 <output_collection name="discarded" count="2"> |
|
5
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
173 <element name="R1"> |
|
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
174 <assert_contents> |
|
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
175 <has_size value="1101516" delta="200"/> |
|
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
176 <has_text text="@lane1_fakedata0_11 1:N:0:"/> |
|
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
177 </assert_contents> |
|
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
178 </element> |
|
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
179 <element name="R2"> |
|
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
180 <assert_contents> |
|
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
181 <has_size value="1613724" delta="200"/> |
|
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
182 <has_text text="@lane1_fakedata0_0 1:N:0:"/> |
|
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
183 </assert_contents> |
|
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
184 </element> |
|
0
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
185 </output_collection> |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
186 </test> |
|
5
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
187 <!-- 03 paired input, no quality but length filter, gzfasta output --> |
|
2
bdd7e518c7d0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents:
1
diff
changeset
|
188 <test expect_num_outputs="4"> |
|
0
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
189 <param name="input_type|input_type_select" value="paired"/> |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
190 <param name="input_type|fqinputs"> |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
191 <collection type="list:paired"> |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
192 <element name="reads"> |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
193 <collection type="paired"> |
|
5
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
194 <element name="forward" value="procrad/R1.fq.gzip" ftype="fastqsanger"/> |
|
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
195 <element name="reverse" value="procrad/R2.fq.gzip" ftype="fastqsanger"/> |
|
0
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
196 </collection> |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
197 </element> |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
198 </collection> |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
199 </param> |
|
5
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
200 <param name="input_type|barcode" value="procrad/barcodes"/> |
|
0
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
201 <param name="options_enzyme|options_enzyme_selector" value="1"/> |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
202 <param name="options_enzyme|enzyme" value="ecoRI"/> |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
203 <param name="filter_cond|filter_select" value="no"/> |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
204 <param name="filter_cond|len_limit" value="50"/> |
|
1
56f6477cf37b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit c300b84615660459bb0020fa74ccd3b874d329a4"
iuc
parents:
0
diff
changeset
|
205 <param name="capture" value="-D"/> |
|
0
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
206 <param name="outype" value="gzfasta"/> |
|
2
bdd7e518c7d0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents:
1
diff
changeset
|
207 <param name="add_log" value="yes"/> |
|
0
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
208 <output name="output_log" file="procrad/process_radtags_paired.out" lines_diff="4"/> |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
209 <assert_command> |
|
2
bdd7e518c7d0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents:
1
diff
changeset
|
210 <has_text text="--len_limit 50"/> |
|
0
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
211 </assert_command> |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
212 <output_collection name="demultiplexed_paired" type="list:paired" count="40"> |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
213 <element name="PopA_01"> |
|
2
bdd7e518c7d0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents:
1
diff
changeset
|
214 <element name="forward" value="demultiplexed/PopA_01.1.fa.gz" ftype="fasta.gz"/> |
|
bdd7e518c7d0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents:
1
diff
changeset
|
215 <element name="reverse" value="demultiplexed/PopA_01.2.fa.gz" ftype="fasta.gz"/> |
|
0
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
216 </element> |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
217 </output_collection> |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
218 <output_collection name="remaining" type="list:paired" count="40"> |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
219 <element name="PopA_01"> |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
220 <element name="forward" file="demultiplexed/PopA_01.rem.1.fa.gz" ftype="fasta.gz"/> |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
221 <element name="reverse" file="demultiplexed/PopA_01.rem.2.fa.gz" ftype="fasta.gz"/> |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
222 </element> |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
223 </output_collection> |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
224 <output_collection name="discarded_paired" type="list:paired" count="1"> |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
225 <element name="reads"> |
|
5
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
226 <element name="forward"> |
|
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
227 <assert_contents> |
|
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
228 <has_size value="609382" delta="200"/> |
|
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
229 <has_text text=">lane1_fakedata0_11 1:N:0:"/> |
|
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
230 </assert_contents> |
|
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
231 </element> |
|
0
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
232 <element name="reverse" file="procrad/R2.fa.discards" ftype="fasta"/> |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
233 </element> |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
234 </output_collection> |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
235 </test> |
|
5
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
236 <!-- 04 paired input (gzipped) + advanced options + two enzymes, fasta output --> |
|
2
bdd7e518c7d0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents:
1
diff
changeset
|
237 <test expect_num_outputs="3"> |
|
0
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
238 <param name="input_type|input_type_select" value="paired"/> |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
239 <param name="input_type|fqinputs"> |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
240 <collection type="list:paired"> |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
241 <element name="reads"> |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
242 <collection type="paired"> |
|
2
bdd7e518c7d0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents:
1
diff
changeset
|
243 <element name="forward" value="procrad/R1.fq.gzip" ftype="fastqsanger.gz"/> |
|
0
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
244 <element name="reverse" value="procrad/R2.fq.gzip" ftype="fastqsanger.gz"/> |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
245 </collection> |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
246 </element> |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
247 </collection> |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
248 </param> |
|
5
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
249 <param name="input_type|barcode" value="procrad/barcodes"/> |
|
0
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
250 <param name="options_enzyme|options_enzyme_selector" value="2"/> |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
251 <param name="options_enzyme|enzyme" value="ecoRI"/> |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
252 <param name="options_enzyme|enzyme2" value="ecoRI"/> |
|
2
bdd7e518c7d0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents:
1
diff
changeset
|
253 <param name="options_advanced|truncate" value="70"/> |
|
0
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
254 <param name="options_advanced|rescue_cond|rescue" value="-r"/> |
|
2
bdd7e518c7d0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents:
1
diff
changeset
|
255 <param name="options_advanced|rescue_cond|barcode_dist_1" value="2"/> |
|
bdd7e518c7d0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents:
1
diff
changeset
|
256 <param name="options_advanced|rescue_cond|barcode_dist_2" value="2"/> |
|
bdd7e518c7d0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents:
1
diff
changeset
|
257 <param name="options_advanced|bestrad" value="--bestrad"/> |
|
1
56f6477cf37b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit c300b84615660459bb0020fa74ccd3b874d329a4"
iuc
parents:
0
diff
changeset
|
258 <param name="options_advanced|retain_header" value="--retain_header"/> |
|
2
bdd7e518c7d0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents:
1
diff
changeset
|
259 <param name="options_advanced|disable_rad_check" value="--disable_rad_check"/> |
|
bdd7e518c7d0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents:
1
diff
changeset
|
260 <param name="options_advanced|adapter_1" value="AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA"/> |
|
bdd7e518c7d0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents:
1
diff
changeset
|
261 <param name="options_advanced|adapter_2" value="TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT"/> |
|
bdd7e518c7d0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents:
1
diff
changeset
|
262 <param name="options_advanced|adapter_mm" value="2"/> |
|
0
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
263 <param name="outype" value="fasta"/> |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
264 <assert_command> |
|
2
bdd7e518c7d0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents:
1
diff
changeset
|
265 <has_text text="-e ecoRI"/> |
|
bdd7e518c7d0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents:
1
diff
changeset
|
266 <has_text text="--renz_2 ecoRI"/> |
|
bdd7e518c7d0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents:
1
diff
changeset
|
267 <has_text text="-t 70"/> |
|
bdd7e518c7d0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents:
1
diff
changeset
|
268 <has_text text="-r"/> |
|
bdd7e518c7d0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents:
1
diff
changeset
|
269 <has_text text="--bestrad"/> |
|
bdd7e518c7d0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents:
1
diff
changeset
|
270 <has_text text="--retain_header"/> |
|
bdd7e518c7d0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents:
1
diff
changeset
|
271 <has_text text="--disable_rad_check"/> |
|
bdd7e518c7d0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents:
1
diff
changeset
|
272 <has_text text="--barcode_dist_1 2"/> |
|
bdd7e518c7d0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents:
1
diff
changeset
|
273 <has_text text="--barcode_dist_2 2"/> |
|
bdd7e518c7d0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents:
1
diff
changeset
|
274 <has_text text="--adapter_1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA"/> |
|
bdd7e518c7d0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents:
1
diff
changeset
|
275 <has_text text="--adapter_2 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT"/> |
|
bdd7e518c7d0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents:
1
diff
changeset
|
276 <has_text text="--adapter_mm 2"/> |
|
0
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
277 </assert_command> |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
278 <output_collection name="demultiplexed_paired" type="list:paired" count="40"> |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
279 <element name="PopA_01"> |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
280 <element name="forward" file="demultiplexed/PopA_01.1.fa" ftype="fasta"/> |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
281 <element name="reverse" file="demultiplexed/PopA_01.2.fa" ftype="fasta"/> |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
282 </element> |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
283 </output_collection> |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
284 <output_collection name="remaining" type="list:paired" count="40"> |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
285 <element name="PopA_01"> |
|
2
bdd7e518c7d0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents:
1
diff
changeset
|
286 <element name="forward" file="demultiplexed/PopA_01.rem.1.fa" ftype="fasta"/> |
|
bdd7e518c7d0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents:
1
diff
changeset
|
287 <element name="reverse" file="demultiplexed/PopA_01.rem.2.fa" ftype="fasta"/> |
|
0
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
288 </element> |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
289 </output_collection> |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
290 </test> |
|
5
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
291 <!-- 05 test invalid barcode file --> |
|
2
bdd7e518c7d0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents:
1
diff
changeset
|
292 <test expect_failure="true"> |
|
bdd7e518c7d0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents:
1
diff
changeset
|
293 <param name="input_type|input_type_select" value="single"/> |
|
5
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
294 <param name="input_type|fqinputs" ftype="fastqsanger" value="procrad/R1_01.fq,procrad/R1_02.fq,procrad/R1_03.fq,procrad/R1_04.fq"/> |
|
2
bdd7e518c7d0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents:
1
diff
changeset
|
295 <param name="input_type|barcode_encoding" value="--inline_null"/> |
|
5
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
296 <param name="input_type|barcode" value="procrad/barcodes-duplicate"/> |
|
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
297 <param name="options_enzyme|options_enzyme_selector" value="1"/> |
|
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
298 <param name="options_enzyme|enzyme" value="ecoRI"/> |
|
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
299 <param name="add_log" value="yes"/> |
|
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
300 </test> |
|
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
301 <!-- 06 test invalid barcode file --> |
|
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
302 <test expect_failure="true"> |
|
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
303 <param name="input_type|input_type_select" value="single"/> |
|
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
304 <param name="input_type|fqinputs" ftype="fastqsanger" value="procrad/R1_01.fq,procrad/R1_02.fq,procrad/R1_03.fq,procrad/R1_04.fq"/> |
|
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
305 <param name="input_type|barcode_encoding" value="--inline_null"/> |
|
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
306 <param name="input_type|barcode" value="procrad/barcodes-duplicate2"/> |
|
2
bdd7e518c7d0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents:
1
diff
changeset
|
307 <param name="options_enzyme|options_enzyme_selector" value="1"/> |
|
bdd7e518c7d0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents:
1
diff
changeset
|
308 <param name="options_enzyme|enzyme" value="ecoRI"/> |
|
bdd7e518c7d0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents:
1
diff
changeset
|
309 <param name="add_log" value="yes"/> |
|
bdd7e518c7d0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents:
1
diff
changeset
|
310 </test> |
|
5
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
311 <!-- 07 test no provided barcode file single--> |
|
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
312 <test expect_num_outputs="3"> |
|
2
bdd7e518c7d0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents:
1
diff
changeset
|
313 <param name="input_type|input_type_select" value="single"/> |
|
5
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
314 <param name="input_type|fqinputs" ftype="fastqsanger.gz" value="procrad/R1.fq.gzip"/> |
|
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
315 <param name="input_type|barcode_encoding" value=""/> |
|
2
bdd7e518c7d0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents:
1
diff
changeset
|
316 <param name="options_enzyme|options_enzyme_selector" value="1"/> |
|
bdd7e518c7d0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents:
1
diff
changeset
|
317 <param name="options_enzyme|enzyme" value="ecoRI"/> |
|
bdd7e518c7d0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents:
1
diff
changeset
|
318 <param name="add_log" value="yes"/> |
|
5
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
319 <param name="capture" value="-D"/> |
|
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
320 <output name="output_log"> |
|
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
321 <assert_contents> |
|
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
322 <has_text text="Barcode Not Found"/> |
|
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
323 <has_text text="Retained Reads"/> |
|
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
324 <has_n_lines n="10"/> |
|
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
325 </assert_contents> |
|
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
326 </output> |
|
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
327 <output_collection name="processed" count="1"> |
|
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
328 <element name="R1"> |
|
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
329 <assert_contents> |
|
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
330 <has_size value="20"/> |
|
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
331 </assert_contents> |
|
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
332 </element> |
|
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
333 </output_collection> |
|
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
334 <output_collection name="discarded" count="1"> |
|
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
335 <element name="R1"> |
|
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
336 <assert_contents> |
|
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
337 <has_size value="1613724" delta="200"/> |
|
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
338 </assert_contents> |
|
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
339 </element> |
|
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
340 </output_collection> |
|
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
341 </test> |
|
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
342 <!-- 08 test no provided barcode file paired --> |
|
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
343 <test expect_num_outputs="3"> |
|
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
344 <param name="input_type|input_type_select" value="paired"/> |
|
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
345 <param name="input_type|fqinputs"> |
|
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
346 <collection type="list:paired"> |
|
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
347 <element name="reads"> |
|
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
348 <collection type="paired"> |
|
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
349 <element name="forward" value="procrad/R1.fq.gzip" ftype="fastqsanger.gz"/> |
|
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
350 <element name="reverse" value="procrad/R2.fq.gzip" ftype="fastqsanger.gz"/> |
|
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
351 </collection> |
|
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
352 </element> |
|
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
353 </collection> |
|
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
354 </param> |
|
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
355 <param name="input_type|barcode_encoding" value=""/> |
|
2
bdd7e518c7d0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents:
1
diff
changeset
|
356 <param name="options_enzyme|options_enzyme_selector" value="1"/> |
|
bdd7e518c7d0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents:
1
diff
changeset
|
357 <param name="options_enzyme|enzyme" value="ecoRI"/> |
|
5
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
358 <param name="outype" value="gzfasta"/> |
|
2
bdd7e518c7d0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents:
1
diff
changeset
|
359 <param name="add_log" value="yes"/> |
|
5
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
360 <output name="output_log" file="procrad/process_radtags_paired_no_barcode.out" lines_diff="4"/> |
|
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
361 <output_collection name="processed_paired" type="list:paired" count="2"> |
|
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
362 <element name="reads_R1_0"> |
|
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
363 <element name="forward"> |
|
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
364 <assert_contents> |
|
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
365 <has_size value="20"/> |
|
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
366 </assert_contents> |
|
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
367 </element> |
|
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
368 </element> |
|
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
369 <element name="reads_R2_0"> |
|
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
370 <element name="reverse"> |
|
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
371 <assert_contents> |
|
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
372 <has_size value="20"/> |
|
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
373 </assert_contents> |
|
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
374 </element> |
|
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
375 </element> |
|
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
376 </output_collection> |
|
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
377 <output_collection name="remaining" type="list:paired" count="2"> |
|
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
378 <element name="reads_R1_0"> |
|
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
379 <element name="forward"> |
|
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
380 <assert_contents> |
|
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
381 <has_size value="20"/> |
|
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
382 </assert_contents> |
|
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
383 </element> |
|
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
384 </element> |
|
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
385 <element name="reads_R2_0"> |
|
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
386 <element name="reverse"> |
|
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
387 <assert_contents> |
|
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
388 <has_size value="17607" delta="100"/> |
|
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
389 </assert_contents> |
|
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
390 </element> |
|
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
391 </element> |
|
02be7d7634b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
392 </output_collection> |
|
2
bdd7e518c7d0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents:
1
diff
changeset
|
393 </test> |
|
0
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
394 </tests> |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
395 <help> |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
396 <![CDATA[ |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
397 .. class:: infomark |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
398 |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
399 **What it does** |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
400 |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
401 This program examines raw reads from an Illumina sequencing run and first, checks that the barcode and the RAD cutsite are intact, and demultiplexes the data. If there are errors in the barcode or the RAD site within a certain allowance process_radtags can correct them. Second, it slides a window down the length of the read and checks the average quality score within the window. If the score drops below 90% probability of being correct (a raw phred score of 10), the read is discarded. This allows for some seqeuncing errors while elimating reads where the sequence is degrading as it is being sequenced. By default the sliding window is 15% of the length of the read, but the threshold and window size can be adjusted. |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
402 |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
403 The process_radtags program can: |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
404 |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
405 - handle data that is barcoded, either inline or using an index, or unbarcoded. |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
406 - use combinatorial barcodes. |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
407 - check and correct for a restriction enzyme cutsite for single or double-digested data. |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
408 - filter adapter sequence while allowing for sequencing error in the adapter pattern. |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
409 - process individual files or whole directories of files. |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
410 - directly read gzipped data |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
411 - filter reads based on Illumina's Chastity filter |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
412 |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
413 **Help** |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
414 |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
415 Input files: |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
416 |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
417 - A set of one or more FASTQ files (either selected manually, a dataset list, or a paired dataset list) |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
418 |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
419 - Barcode File |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
420 |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
421 The barcode file is a very simple format: |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
422 |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
423 ======= =========== |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
424 Barcode Sample name |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
425 ======= =========== |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
426 ATGGGG PopA_01 |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
427 GGGTAA PopA_02 |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
428 AGGAAA PopA_03 |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
429 TTTAAG PopA_04 |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
430 GGTGTG PopA_05 |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
431 TGATGT PopA_06 |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
432 ======= =========== |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
433 |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
434 Combinatorial barcodes are specified, one per column, separated by a tab: |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
435 |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
436 ======== ======== =========== |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
437 Barcode1 Barcode2 Sample name |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
438 ======== ======== =========== |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
439 CGATA ACGTA PopA_01 |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
440 CGGCG CGTA PopA_02 |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
441 GAAGC CGTA PopA_03 |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
442 GAGAT CGTA PopA_04 |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
443 CGATA AGCA PopA_05 |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
444 CGGCG AGCA PopA_06 |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
445 ======== ======== =========== |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
446 |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
447 The sample name column can be omitted. Then the Barcodes are used for naming the output files. |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
448 |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
449 @STACKS_INFOS@ |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
450 ]]> |
|
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
451 </help> |
|
2
bdd7e518c7d0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents:
1
diff
changeset
|
452 <expand macro="citation"/> |
|
0
3d413e8cb277
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
453 </tool> |