Mercurial > repos > petr-novak > dante_ltr

annotate clean_dante_ltr.xml @ 17:d1c3b29b1478 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit ce025ba66edc87ff8ced32d5fdb36109f12cebf0-dirty
author petr-novak
date Thu, 10 Aug 2023 12:22:28 +0000
parents 7ec262f92d89
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
17
d1c3b29b1478 planemo upload commit ce025ba66edc87ff8ced32d5fdb36109f12cebf0-dirty
petr-novak
parents: 16
diff changeset
1 <tool id="clean_dante_ltr" name="DANTE_LTR retrotransposons filtering" version="@TOOL_VERSION@" python_template_version="3.5">
d1c3b29b1478 planemo upload commit ce025ba66edc87ff8ced32d5fdb36109f12cebf0-dirty
petr-novak
parents: 16
diff changeset
2 <macros>
d1c3b29b1478 planemo upload commit ce025ba66edc87ff8ced32d5fdb36109f12cebf0-dirty
petr-novak
parents: 16
diff changeset
3 <import>macros.xml</import>
d1c3b29b1478 planemo upload commit ce025ba66edc87ff8ced32d5fdb36109f12cebf0-dirty
petr-novak
parents: 16
diff changeset
4 </macros>
d1c3b29b1478 planemo upload commit ce025ba66edc87ff8ced32d5fdb36109f12cebf0-dirty
petr-novak
parents: 16
diff changeset
5 <expand macro="requirements" />
0
7b0bbe7477c4 "planemo upload commit 92c684dff3b377c8c08654c7f3d46a133385e3e0-dirty"
petr-novak
parents:
diff changeset
6 <command detect_errors="exit_code"><![CDATA[
14
3b3a87915ef6 "planemo upload commit 2b4592de91793d6bbe4182d4ca9ee749d361fd82-dirty"
petr-novak
parents: 13
diff changeset
7 clean_ltr.R --gff3 '$dante_ltr' --reference_sequence '$reference' --output output --cpu \${GALAXY_SLOTS:-1}
0
7b0bbe7477c4 "planemo upload commit 92c684dff3b377c8c08654c7f3d46a133385e3e0-dirty"
petr-novak
parents:
diff changeset
8 &&
7b0bbe7477c4 "planemo upload commit 92c684dff3b377c8c08654c7f3d46a133385e3e0-dirty"
petr-novak
parents:
diff changeset
9 mv output_clean.gff3 $dante_ltr_clean
7b0bbe7477c4 "planemo upload commit 92c684dff3b377c8c08654c7f3d46a133385e3e0-dirty"
petr-novak
parents:
diff changeset
10 &&
3
6ae4a341d1f3 "planemo upload commit 8bd6029a4de4a8f5031a5cc71303bb06217cc88a"
petr-novak
parents: 2
diff changeset
11 mv output_RM_lib_non_redundant.fasta $rm_lib
6ae4a341d1f3 "planemo upload commit 8bd6029a4de4a8f5031a5cc71303bb06217cc88a"
petr-novak
parents: 2
diff changeset
12 &&
6ae4a341d1f3 "planemo upload commit 8bd6029a4de4a8f5031a5cc71303bb06217cc88a"
petr-novak
parents: 2
diff changeset
13 mv output_RM_lib_full_TE.fasta $te_full
6ae4a341d1f3 "planemo upload commit 8bd6029a4de4a8f5031a5cc71303bb06217cc88a"
petr-novak
parents: 2
diff changeset
14 &&
6ae4a341d1f3 "planemo upload commit 8bd6029a4de4a8f5031a5cc71303bb06217cc88a"
petr-novak
parents: 2
diff changeset
15 mv output_RM_lib_5LTR.fasta $ltr5
6ae4a341d1f3 "planemo upload commit 8bd6029a4de4a8f5031a5cc71303bb06217cc88a"
petr-novak
parents: 2
diff changeset
16 &&
6ae4a341d1f3 "planemo upload commit 8bd6029a4de4a8f5031a5cc71303bb06217cc88a"
petr-novak
parents: 2
diff changeset
17 mv output_RM_lib_3LTR.fasta $ltr3
6ae4a341d1f3 "planemo upload commit 8bd6029a4de4a8f5031a5cc71303bb06217cc88a"
petr-novak
parents: 2
diff changeset
18 &&
6ae4a341d1f3 "planemo upload commit 8bd6029a4de4a8f5031a5cc71303bb06217cc88a"
petr-novak
parents: 2
diff changeset
19 mv output_summary.pdf $summary
0
7b0bbe7477c4 "planemo upload commit 92c684dff3b377c8c08654c7f3d46a133385e3e0-dirty"
petr-novak
parents:
diff changeset
20 ]]></command>
7b0bbe7477c4 "planemo upload commit 92c684dff3b377c8c08654c7f3d46a133385e3e0-dirty"
petr-novak
parents:
diff changeset
21 <inputs>
6
b91ca438a1cb "planemo upload commit 9633fb98932151f059ce02a0ce202a4374ef8d68"
petr-novak
parents: 3
diff changeset
22 <param type="data" name="dante_ltr" format="gff3"
b91ca438a1cb "planemo upload commit 9633fb98932151f059ce02a0ce202a4374ef8d68"
petr-novak
parents: 3
diff changeset
23 label="GFF3 output from DANTE_LTR retrotransposon identification pipeline"/>
b91ca438a1cb "planemo upload commit 9633fb98932151f059ce02a0ce202a4374ef8d68"
petr-novak
parents: 3
diff changeset
24 <param type="data" name="reference" format="fasta" label="Reference sequence matching input GFF3" />
0
7b0bbe7477c4 "planemo upload commit 92c684dff3b377c8c08654c7f3d46a133385e3e0-dirty"
petr-novak
parents:
diff changeset
25 </inputs>
7b0bbe7477c4 "planemo upload commit 92c684dff3b377c8c08654c7f3d46a133385e3e0-dirty"
petr-novak
parents:
diff changeset
26 <outputs>
6
b91ca438a1cb "planemo upload commit 9633fb98932151f059ce02a0ce202a4374ef8d68"
petr-novak
parents: 3
diff changeset
27 <data name="dante_ltr_clean" format="gff3"
b91ca438a1cb "planemo upload commit 9633fb98932151f059ce02a0ce202a4374ef8d68"
petr-novak
parents: 3
diff changeset
28 label="Validated LTR retrotransposons annotation (GFF3) based on annotation
b91ca438a1cb "planemo upload commit 9633fb98932151f059ce02a0ce202a4374ef8d68"
petr-novak
parents: 3
diff changeset
29 $dante_ltr.hid and reference $reference.hid"/>
b91ca438a1cb "planemo upload commit 9633fb98932151f059ce02a0ce202a4374ef8d68"
petr-novak
parents: 3
diff changeset
30 <data name="rm_lib" format="fasta" label="Non-redundant library of LTR retrotransposons (FASTA) based on annotation $dante_ltr.hid and reference $reference.hid"/>
3
6ae4a341d1f3 "planemo upload commit 8bd6029a4de4a8f5031a5cc71303bb06217cc88a"
petr-novak
parents: 2
diff changeset
31
12
ff01d4263391 "planemo upload commit 414119ad7c44562d2e956b765e97ca113bc35b2b-dirty"
petr-novak
parents: 8
diff changeset
32 <data name="te_full" format="fasta" label="Library of LTR retrotransposons (FASTA) based on annotation $dante_ltr.hid and reference $reference.hid"/>
6
b91ca438a1cb "planemo upload commit 9633fb98932151f059ce02a0ce202a4374ef8d68"
petr-novak
parents: 3
diff changeset
33
b91ca438a1cb "planemo upload commit 9633fb98932151f059ce02a0ce202a4374ef8d68"
petr-novak
parents: 3
diff changeset
34 <data name="ltr5" format="fasta" label="Library of 5'LTR of retrotransposons (FASTA) based on annotation $dante_ltr.hid and reference $reference.hid"/>
3
6ae4a341d1f3 "planemo upload commit 8bd6029a4de4a8f5031a5cc71303bb06217cc88a"
petr-novak
parents: 2
diff changeset
35
6
b91ca438a1cb "planemo upload commit 9633fb98932151f059ce02a0ce202a4374ef8d68"
petr-novak
parents: 3
diff changeset
36 <data name="ltr3" format="fasta" label="Library of 3'LTR of retrotransposons (FASTA) based on annotation $dante_ltr.hid and reference $reference.hid"/>
3
6ae4a341d1f3 "planemo upload commit 8bd6029a4de4a8f5031a5cc71303bb06217cc88a"
petr-novak
parents: 2
diff changeset
37
6
b91ca438a1cb "planemo upload commit 9633fb98932151f059ce02a0ce202a4374ef8d68"
petr-novak
parents: 3
diff changeset
38 <data name="summary" format="pdf" label="LTR retrotransposons lengths summary based on $dante_ltr.hid and reference $reference.hid"/>
3
6ae4a341d1f3 "planemo upload commit 8bd6029a4de4a8f5031a5cc71303bb06217cc88a"
petr-novak
parents: 2
diff changeset
39
0
7b0bbe7477c4 "planemo upload commit 92c684dff3b377c8c08654c7f3d46a133385e3e0-dirty"
petr-novak
parents:
diff changeset
40 </outputs>
7b0bbe7477c4 "planemo upload commit 92c684dff3b377c8c08654c7f3d46a133385e3e0-dirty"
petr-novak
parents:
diff changeset
41 <help><![CDATA[
6
b91ca438a1cb "planemo upload commit 9633fb98932151f059ce02a0ce202a4374ef8d68"
petr-novak
parents: 3
diff changeset
42 This tool takes output from DANTE_LTR search identifies good quality retrotransposons.
b91ca438a1cb "planemo upload commit 9633fb98932151f059ce02a0ce202a4374ef8d68"
petr-novak
parents: 3
diff changeset
43 Good quality retrotransposons are considered those which does not have any cross-similarity between distinct lineages.
0
7b0bbe7477c4 "planemo upload commit 92c684dff3b377c8c08654c7f3d46a133385e3e0-dirty"
petr-novak
parents:
diff changeset
44 Output from this tool is a annotation in GFF3 format and
6
b91ca438a1cb "planemo upload commit 9633fb98932151f059ce02a0ce202a4374ef8d68"
petr-novak
parents: 3
diff changeset
45 libraries of elements for custom RepeatMasker search.
0
7b0bbe7477c4 "planemo upload commit 92c684dff3b377c8c08654c7f3d46a133385e3e0-dirty"
petr-novak
parents:
diff changeset
46
7b0bbe7477c4 "planemo upload commit 92c684dff3b377c8c08654c7f3d46a133385e3e0-dirty"
petr-novak
parents:
diff changeset
47 ]]></help>
7b0bbe7477c4 "planemo upload commit 92c684dff3b377c8c08654c7f3d46a133385e3e0-dirty"
petr-novak
parents:
diff changeset
48 </tool>