Mercurial > repos > iuc > bax2bam
annotate bax2bam.xml @ 0:4445939cacc9 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
author | iuc |
---|---|
date | Sat, 12 Oct 2019 06:52:23 -0400 |
parents | |
children | ee356d7a5518 |
rev | line source |
---|---|
0
4445939cacc9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
iuc
parents:
diff
changeset
|
1 <?xml version="1.0"?> |
4445939cacc9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
iuc
parents:
diff
changeset
|
2 <tool id="bax2bam" name="bax2bam" version="@TOOL_VERSION@+@WRAPPER_VERSION@"> |
4445939cacc9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
iuc
parents:
diff
changeset
|
3 <description>converts PacBio basecall format (bax.h5) into BAM</description> |
4445939cacc9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
iuc
parents:
diff
changeset
|
4 <macros> |
4445939cacc9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
iuc
parents:
diff
changeset
|
5 <import>macros.xml</import> |
4445939cacc9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
iuc
parents:
diff
changeset
|
6 </macros> |
4445939cacc9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
iuc
parents:
diff
changeset
|
7 <expand macro="requirements"/> |
4445939cacc9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
iuc
parents:
diff
changeset
|
8 <stdio></stdio> |
4445939cacc9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
iuc
parents:
diff
changeset
|
9 <command detect_errors="exit_code"><![CDATA[ |
4445939cacc9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
iuc
parents:
diff
changeset
|
10 bax2bam |
4445939cacc9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
iuc
parents:
diff
changeset
|
11 #for $file in $files |
4445939cacc9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
iuc
parents:
diff
changeset
|
12 '$file' |
4445939cacc9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
iuc
parents:
diff
changeset
|
13 #end for |
4445939cacc9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
iuc
parents:
diff
changeset
|
14 -o output |
4445939cacc9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
iuc
parents:
diff
changeset
|
15 $readtype |
4445939cacc9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
iuc
parents:
diff
changeset
|
16 #if $pulsefeatures |
4445939cacc9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
iuc
parents:
diff
changeset
|
17 --pulsefeatures=$pulsefeatures |
4445939cacc9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
iuc
parents:
diff
changeset
|
18 #end if |
4445939cacc9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
iuc
parents:
diff
changeset
|
19 $losslessframes |
4445939cacc9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
iuc
parents:
diff
changeset
|
20 $internal |
4445939cacc9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
iuc
parents:
diff
changeset
|
21 ]]></command> |
4445939cacc9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
iuc
parents:
diff
changeset
|
22 <inputs> |
4445939cacc9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
iuc
parents:
diff
changeset
|
23 <param name="files" type="data" format="h5" multiple="true" label="Files" help="Should be from the same movie."/> |
4445939cacc9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
iuc
parents:
diff
changeset
|
24 <param name="readtype" type="select" label="Output read type" help=""> |
4445939cacc9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
iuc
parents:
diff
changeset
|
25 <option value="--subread">subread</option> |
4445939cacc9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
iuc
parents:
diff
changeset
|
26 <option value="--hqregion">hqregion</option> |
4445939cacc9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
iuc
parents:
diff
changeset
|
27 <option value="--polymeraseread">polymeraseread</option> |
4445939cacc9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
iuc
parents:
diff
changeset
|
28 </param> |
4445939cacc9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
iuc
parents:
diff
changeset
|
29 <param argument="--pulsefeatures" type="select" multiple="true" label="Select pulse features in the output BAM." help=""> |
4445939cacc9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
iuc
parents:
diff
changeset
|
30 <option value="DeletionQV" selected="true">dq - DeletionQV</option> |
4445939cacc9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
iuc
parents:
diff
changeset
|
31 <option value="DeletionTag" selected="true">dt - DeletionTag</option> |
4445939cacc9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
iuc
parents:
diff
changeset
|
32 <option value="InsertionQV" selected="true">iq - InsertionQV</option> |
4445939cacc9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
iuc
parents:
diff
changeset
|
33 <option value="IPD" selected="true">ip - IPD</option> |
4445939cacc9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
iuc
parents:
diff
changeset
|
34 <option value="PulseWidth" selected="true">pw - PulseWidth</option> |
4445939cacc9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
iuc
parents:
diff
changeset
|
35 <option value="MergeQV" selected="true">mq - MergeQV</option> |
4445939cacc9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
iuc
parents:
diff
changeset
|
36 <option value="SubstitutionQV" selected="true">sq - SubstitutionQV</option> |
4445939cacc9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
iuc
parents:
diff
changeset
|
37 <option value="SubstitutionTag" selected="false">st - SubstitutionTag</option> |
4445939cacc9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
iuc
parents:
diff
changeset
|
38 </param> |
4445939cacc9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
iuc
parents:
diff
changeset
|
39 <param argument="--losslessframes" type="boolean" truevalue="--losslessframes" falsevalue="" checked="false" label="Store full, 16-bit IPD/PulseWidth data" help="Instead of (default) downsampled, 8-bit encoding."/> |
4445939cacc9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
iuc
parents:
diff
changeset
|
40 <param argument="--internal" type="boolean" truevalue="--internal" falsevalue="" checked="false" label="Output BAMs in internal mode." help="Currently this indicates that non-sequencing ZMWs should be included in the output scraps BAM file, if applicable."/> |
4445939cacc9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
iuc
parents:
diff
changeset
|
41 </inputs> |
4445939cacc9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
iuc
parents:
diff
changeset
|
42 |
4445939cacc9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
iuc
parents:
diff
changeset
|
43 <outputs> |
4445939cacc9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
iuc
parents:
diff
changeset
|
44 <data name="output_scrap" from_work_dir="output.scraps.bam" format="bam" label="${tool.name} on ${on_string}: scraps"> |
4445939cacc9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
iuc
parents:
diff
changeset
|
45 <filter>readtype == '--subread'</filter> |
4445939cacc9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
iuc
parents:
diff
changeset
|
46 </data> |
4445939cacc9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
iuc
parents:
diff
changeset
|
47 <data name="output_subread" from_work_dir="output.subreads.bam" format="bam" label="${tool.name} on ${on_string}: subreads"> |
4445939cacc9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
iuc
parents:
diff
changeset
|
48 <filter>readtype == '--subread'</filter> |
4445939cacc9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
iuc
parents:
diff
changeset
|
49 </data> |
4445939cacc9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
iuc
parents:
diff
changeset
|
50 <data name="output_hqregion" from_work_dir="output.hqregions.bam" format="bam" label="${tool.name} on ${on_string}: hqregions"> |
4445939cacc9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
iuc
parents:
diff
changeset
|
51 <filter>readtype == '--hqregion'</filter> |
4445939cacc9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
iuc
parents:
diff
changeset
|
52 </data> |
4445939cacc9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
iuc
parents:
diff
changeset
|
53 <data name="output_lqregion" from_work_dir="output.lqregions.bam" format="bam" label="${tool.name} on ${on_string}: lqregions"> |
4445939cacc9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
iuc
parents:
diff
changeset
|
54 <filter>readtype == '--hqregion'</filter> |
4445939cacc9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
iuc
parents:
diff
changeset
|
55 </data> |
4445939cacc9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
iuc
parents:
diff
changeset
|
56 <data name="output_polymeraseread" from_work_dir="output.polymerase.bam" format="bam" label="${tool.name} on ${on_string}: polymerase"> |
4445939cacc9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
iuc
parents:
diff
changeset
|
57 <filter>readtype == '--polymeraseread'</filter> |
4445939cacc9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
iuc
parents:
diff
changeset
|
58 </data> |
4445939cacc9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
iuc
parents:
diff
changeset
|
59 </outputs> |
4445939cacc9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
iuc
parents:
diff
changeset
|
60 |
4445939cacc9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
iuc
parents:
diff
changeset
|
61 <tests> |
4445939cacc9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
iuc
parents:
diff
changeset
|
62 <!-- source of test data: https://github.com/PacificBiosciences/PacBioTestData/tree/master/data/HdfSubreadSet/Analysis_Results/ --> |
4445939cacc9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
iuc
parents:
diff
changeset
|
63 <!-- #1: read type: subread --> |
4445939cacc9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
iuc
parents:
diff
changeset
|
64 <test> |
4445939cacc9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
iuc
parents:
diff
changeset
|
65 <param name="files" value="set.3.bax.h5,set.2.bax.h5,set.1.bax.h5"/> |
4445939cacc9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
iuc
parents:
diff
changeset
|
66 <param name="readtype" value="--subread"/> |
4445939cacc9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
iuc
parents:
diff
changeset
|
67 <output name="output_scrap" file="scraps.bam" compare="sim_size" delta="100"/> |
4445939cacc9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
iuc
parents:
diff
changeset
|
68 <output name="output_subread" file="subreads.bam" compare="sim_size" delta="100"/> |
4445939cacc9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
iuc
parents:
diff
changeset
|
69 </test> |
4445939cacc9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
iuc
parents:
diff
changeset
|
70 <!-- #2: read type: hqregion --> |
4445939cacc9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
iuc
parents:
diff
changeset
|
71 <test> |
4445939cacc9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
iuc
parents:
diff
changeset
|
72 <param name="files" value="set.3.bax.h5,set.2.bax.h5,set.1.bax.h5"/> |
4445939cacc9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
iuc
parents:
diff
changeset
|
73 <param name="readtype" value="--hqregion"/> |
4445939cacc9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
iuc
parents:
diff
changeset
|
74 <output name="output_hqregion" file="hqregions.bam" compare="sim_size" delta="100"/> |
4445939cacc9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
iuc
parents:
diff
changeset
|
75 <output name="output_hqregion" file="lqregions.bam" compare="sim_size" delta="100"/> |
4445939cacc9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
iuc
parents:
diff
changeset
|
76 </test> |
4445939cacc9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
iuc
parents:
diff
changeset
|
77 <!-- #3: read type: polymeraseread --> |
4445939cacc9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
iuc
parents:
diff
changeset
|
78 <test> |
4445939cacc9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
iuc
parents:
diff
changeset
|
79 <param name="files" value="set.3.bax.h5,set.2.bax.h5,set.1.bax.h5"/> |
4445939cacc9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
iuc
parents:
diff
changeset
|
80 <param name="readtype" value="--polymeraseread" compare="sim_size" delta="100"/> |
4445939cacc9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
iuc
parents:
diff
changeset
|
81 <output name="output_polymeraseread" file="polymerase.bam" compare="sim_size" delta="100"/> |
4445939cacc9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
iuc
parents:
diff
changeset
|
82 </test> |
4445939cacc9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
iuc
parents:
diff
changeset
|
83 <!-- #4: read type: subread, custom parameters --> |
4445939cacc9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
iuc
parents:
diff
changeset
|
84 <test> |
4445939cacc9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
iuc
parents:
diff
changeset
|
85 <param name="files" value="set.3.bax.h5,set.2.bax.h5,set.1.bax.h5"/> |
4445939cacc9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
iuc
parents:
diff
changeset
|
86 <param name="readtype" value="--subread"/> |
4445939cacc9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
iuc
parents:
diff
changeset
|
87 <param name="pulsefeatures" value="SubstitutionTag"/> |
4445939cacc9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
iuc
parents:
diff
changeset
|
88 <param name="losslessframes" value="true"/> |
4445939cacc9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
iuc
parents:
diff
changeset
|
89 <param name="internal" value="true"/> |
4445939cacc9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
iuc
parents:
diff
changeset
|
90 <output name="output_scrap" file="scraps_custom.bam" compare="sim_size" delta="100"/> |
4445939cacc9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
iuc
parents:
diff
changeset
|
91 <output name="output_subread" file="subreads_custom.bam" compare="sim_size" delta="100"/> |
4445939cacc9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
iuc
parents:
diff
changeset
|
92 </test> |
4445939cacc9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
iuc
parents:
diff
changeset
|
93 </tests> |
4445939cacc9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
iuc
parents:
diff
changeset
|
94 <help><![CDATA[ |
4445939cacc9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
iuc
parents:
diff
changeset
|
95 |
4445939cacc9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
iuc
parents:
diff
changeset
|
96 .. class:: infomark |
4445939cacc9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
iuc
parents:
diff
changeset
|
97 |
4445939cacc9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
iuc
parents:
diff
changeset
|
98 **What it does** |
4445939cacc9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
iuc
parents:
diff
changeset
|
99 |
4445939cacc9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
iuc
parents:
diff
changeset
|
100 bax2bam converts the legacy PacBio basecall format (bax.h5) into the BAM basecall format. |
4445939cacc9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
iuc
parents:
diff
changeset
|
101 |
4445939cacc9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
iuc
parents:
diff
changeset
|
102 **Input** |
4445939cacc9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
iuc
parents:
diff
changeset
|
103 |
4445939cacc9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
iuc
parents:
diff
changeset
|
104 bax.h5 files that should be from the same movie. |
4445939cacc9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
iuc
parents:
diff
changeset
|
105 |
4445939cacc9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
iuc
parents:
diff
changeset
|
106 **Output** |
4445939cacc9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
iuc
parents:
diff
changeset
|
107 |
4445939cacc9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
iuc
parents:
diff
changeset
|
108 A single BAM file. |
4445939cacc9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
iuc
parents:
diff
changeset
|
109 |
4445939cacc9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
iuc
parents:
diff
changeset
|
110 .. class:: infomark |
4445939cacc9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
iuc
parents:
diff
changeset
|
111 |
4445939cacc9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
iuc
parents:
diff
changeset
|
112 **References** |
4445939cacc9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
iuc
parents:
diff
changeset
|
113 |
4445939cacc9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
iuc
parents:
diff
changeset
|
114 More information can be found on the github repositories `bax2bam <https://github.com/pacificbiosciences/bax2bam/>`_ and `PacBio Bioconda <https://github.com/PacificBiosciences/pbbioconda>`_. |
4445939cacc9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
iuc
parents:
diff
changeset
|
115 ]]></help> |
4445939cacc9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
iuc
parents:
diff
changeset
|
116 <citations> |
4445939cacc9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
iuc
parents:
diff
changeset
|
117 <citation type="bibtex"> |
4445939cacc9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
iuc
parents:
diff
changeset
|
118 @misc{PacificBiosciences2018, |
4445939cacc9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
iuc
parents:
diff
changeset
|
119 author = {Pacific Biosciences}, |
4445939cacc9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
iuc
parents:
diff
changeset
|
120 year = {2018}, |
4445939cacc9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
iuc
parents:
diff
changeset
|
121 title = {bax2bam}, |
4445939cacc9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
iuc
parents:
diff
changeset
|
122 publisher = {GitHub}, |
4445939cacc9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
iuc
parents:
diff
changeset
|
123 journal = {GitHub repository}, |
4445939cacc9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
iuc
parents:
diff
changeset
|
124 url = {https://github.com/pacificbiosciences/bax2bam/}, |
4445939cacc9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
iuc
parents:
diff
changeset
|
125 } |
4445939cacc9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
iuc
parents:
diff
changeset
|
126 </citation> |
4445939cacc9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
iuc
parents:
diff
changeset
|
127 </citations> |
4445939cacc9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
iuc
parents:
diff
changeset
|
128 </tool> |