Mercurial > repos > rmarenco > hubarchivecreator
annotate tests.xml @ 30:e7c4be523cb7 draft
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 2f1b3cc8c9cb463e460f7f79efe99ed472700ecf
| author | yating-l |
|---|---|
| date | Tue, 19 Jun 2018 13:02:32 -0400 |
| parents | 7e8a8b732db3 |
| children |
| rev | line source |
|---|---|
|
29
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
1 #if $f.formatChoice.bedChoice.bed_select == "bed_blast_alignment_option" |
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7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
2 #set database = str($f.formatChoice.bedChoice.database) |
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7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
3 #silent $extra_data_dict.update({"database": $database}) |
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7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
4 #if $f.formatChoice.bedChoice.add_trix_index.add_trix_index_selector == "yes" |
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7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
5 #for i in $f.formatChoice.bedChoice.add_trix_index.trix_index |
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7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
6 #if $i.element_identifier.endswith("ix") |
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7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
7 #$extra_data_dict.update({"index_ix": str($i)}) |
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7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
8 #elif $i.element_identifier.endswith("ixx") |
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7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
9 #$extra_data_dict.update({"index_ixx": str($i)}) |
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7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
10 #end if |
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7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
11 #end for |
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7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
12 ##set ix_index = str($f.formatChoice.bedChoice.add_trix_index.trix_index.index_ix) |
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7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
13 ##set ixx_index = str($f.formatChoice.bedChoice.add_trix_index.trix_index.index_ixx) |
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7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
14 ##silent $extra_data_dict.update({"indexIx": $ix_index, "indexIxx": $ixx_index}) |
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7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
15 #end if |
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7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
16 #silent $prepare_json("BedBlastAlignments", $f.formatChoice.bedChoice.BED_blast_alignment, $index_track_final, |
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7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
17 $extra_data_dict) |
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7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
18 #end if |
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7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
19 #if $f.formatChoice.bedChoice.bed_select == "bed_blat_alignment_option" |
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7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
20 #set database = str($f.formatChoice.bedChoice.database) |
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7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
21 #silent $extra_data_dict.update({"database": $database}) |
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7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
22 #if $f.formatChoice.bedChoice.add_trix_index.add_trix_index_selector == "yes" |
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7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
23 #for i in $f.formatChoice.bedChoice.add_trix_index.trix_index |
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7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
24 #if $i.element_identifier.endswith("ix") |
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7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
25 #$extra_data_dict.update({"index_ix": str($i)}) |
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7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
26 #elif $i.element_identifier.endswith("ixx") |
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7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
27 #$extra_data_dict.update({"index_ixx": str($i)}) |
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7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
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28 #end if |
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7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
29 #end for |
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7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
30 ##set ix_index = str($f.formatChoice.bedChoice.add_trix_index.trix_index.index_ix) |
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7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
31 ##set ixx_index = str($f.formatChoice.bedChoice.add_trix_index.trix_index.index_ixx) |
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7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
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32 ##silent $extra_data_dict.update({"indexIx": $ix_index, "indexIxx": $ixx_index}) |
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7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
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33 #end if |
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7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
34 #silent $prepare_json("BedBlatAlignments", $f.formatChoice.bedChoice.BED_blat_alignment, $index_track_final, |
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7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
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35 $extra_data_dict) |
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7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
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36 #end if |
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7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
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37 |
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7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
38 #if $f.formatChoice.format_select == "bigbed" |
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7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
39 #if $f.formatChoice.add_trix_index.add_trix_index_selector == "yes" |
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7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
40 ##set ix_index = str($f.formatChoice.add_trix_index.trix_index.index_ix) |
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7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
41 ##set ixx_index = str($f.formatChoice.add_trix_index.trix_index.index_ixx) |
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7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
42 #for i in $f.formatChoice.add_trix_index.trix_index |
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7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
43 #if $i.element_identifier.endswith("ix") |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
44 #$extra_data_dict.update({"index_ix": str($i)}) |
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7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
45 #elif $i.element_identifier.endswith("ixx") |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
46 #$extra_data_dict.update({"index_ixx": str($i)}) |
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7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
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47 #end if |
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7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
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48 #end for |
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7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
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49 #$extra_data_dict.update({"trix_id": str($f.formatChoice.add_trix_index.trix_id)}) |
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7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
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50 ##set trix_id = str($f.formatChoice.add_trix_index.trix_id) |
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7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
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51 ##silent $extra_data_dict.update({"indexIx": $ix_index, "indexIxx": $ixx_index, "trix_id": $trix_id}) |
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7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
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52 #end if |
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7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
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53 #silent $prepare_json("BigBed", $f.formatChoice.BIGBED, $index_track_final, |
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7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
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54 $extra_data_dict) |
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7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
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55 #end if |
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7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
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56 <!-- Test with only the fasta file --> |
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7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
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57 <test> |
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7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
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58 <param name="genome_name" value="Dbia3"/> |
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7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
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59 <param name="fasta_file" value="common/dbia3.fa"/> |
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7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
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60 <output name="output" file="only_genome/only_genome.html"> |
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7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
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61 <!-- Use macro to check the whole common structure without repeated code --> |
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7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
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62 <expand macro="verify_hub_structure_no_track" test="only_genome" /> |
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7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
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63 </output> |
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7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
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64 </test> |
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7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
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65 |
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7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
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66 <!-- Test with Bam --> |
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7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
67 <test> |
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7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
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68 <param name="genome_name" value="Dbia3"/> |
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7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
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69 <param name="fasta_file" value="common/dbia3.fa"/> |
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7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
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70 <repeat name="group"> |
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7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
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71 <param name="group_name" value="Default group"/> |
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7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
72 <repeat name="format"> |
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7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
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73 <conditional name="formatChoice"> |
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7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
74 <param name="format_select" value="bam"/> |
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7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
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75 <param name="BAM" value="bam/inputs/HISAT2_Accepted_Hits.bam" /> |
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7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
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76 <param name="longLabel" value="HISAT sequence alignment" /> |
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7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
77 <param name="track_color" value="#000000"/> |
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7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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|
78 </conditional> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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|
79 </repeat> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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parents:
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|
80 </repeat> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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|
81 <output name="output" file="bam/bam.html"> |
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7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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|
82 <!-- Verify tracks folder contains bam and bai --> |
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7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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parents:
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|
83 <extra_files type="file" |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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parents:
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changeset
|
84 name="myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam" |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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diff
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|
85 value="bam/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam" |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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|
86 compare="sim_size" |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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parents:
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|
87 /> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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parents:
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|
88 <extra_files type="file" |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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parents:
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|
89 name="myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai" |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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|
90 value="bam/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai" |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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|
91 compare="sim_size" |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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|
92 /> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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|
93 <!-- Use macro to check the whole common structure without repeated code --> |
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7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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|
94 <expand macro="verify_hub_structure" test="bam" /> |
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7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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|
95 </output> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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|
96 </test> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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parents:
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|
97 |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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|
98 <!-- Test with Bed Generic --> |
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7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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|
99 <test> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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|
100 <param name="genome_name" value="Dbia3"/> |
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7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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101 <param name="fasta_file" value="common/dbia3.fa"/> |
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7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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102 <repeat name="group"> |
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7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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103 <param name="group_name" value="Default group"/> |
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7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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104 <repeat name="format"> |
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7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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|
105 <conditional name="formatChoice"> |
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7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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106 <param name="format_select" value="bed" /> |
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7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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107 <conditional name="bedChoice"> |
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7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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108 <param name="bed_select" value="bed_generic"/> |
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7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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109 <param name="BED" ftype="bed" value="bed_generic/inputs/TBLASTN_Alignment_to_proteins"/> |
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7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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|
110 <param name="longLabel" value="TBLASTN alignment" /> |
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7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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|
111 <param name="track_color" value="#000000"/> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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|
112 </conditional> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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|
113 </conditional> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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|
114 </repeat> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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|
115 </repeat> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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116 <output name="output" file="bed_generic/bed_generic.html"> |
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7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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117 <extra_files type="file" |
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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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|
118 name="myHub/Dbia3/tracks/TBLASTN_Alignment_to_proteins.bb" |
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7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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119 value="bed_generic/myHub/Dbia3/tracks/TBLASTN_Alignment_to_proteins.bb" |
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7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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|
120 compare="sim_size" |
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7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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|
121 /> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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|
122 <expand macro="verify_hub_structure" test="bed_generic" /> |
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7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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|
123 </output> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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|
124 </test> |
|
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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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|
125 |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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|
126 <!-- Test with Bed Simple repeat --> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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|
127 <test> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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128 <param name="genome_name" value="Dbia3"/> |
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7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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129 <param name="fasta_file" value="common/dbia3.fa"/> |
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7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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130 <repeat name="group"> |
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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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131 <param name="group_name" value="Default group"/> |
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7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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132 <repeat name="format"> |
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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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133 <conditional name="formatChoice"> |
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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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134 <param name="format_select" value="bed" /> |
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7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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135 <conditional name="bedChoice"> |
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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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136 <param name="bed_select" value="bed_simple_repeats_option"/> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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137 <param name="BED_simple_repeats" ftype="bed" value="bed_simple_repeats/inputs/Repeating_Elements_by_TrfBig"/> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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138 <param name="longLabel" value="Simple repeat" /> |
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7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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139 <param name="track_color" value="#000000"/> |
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7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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|
140 </conditional> |
|
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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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141 </conditional> |
|
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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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|
142 </repeat> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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|
143 </repeat> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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144 <output name="output" file="bed_simple_repeats/bed_simple_repeats_trackhub.html"> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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145 <extra_files type="file" |
|
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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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146 name="myHub/Dbia3/tracks/Repeating_Elements_by_TrfBig.bb" |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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147 value="bed_simple_repeats/myHub/Dbia3/tracks/Repeating_Elements_by_TrfBig.bb" |
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7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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148 compare="sim_size" |
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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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149 /> |
|
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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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150 <expand macro="verify_hub_structure" test="bed_simple_repeats" /> |
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7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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|
151 </output> |
|
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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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|
152 </test> |
|
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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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|
153 |
|
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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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154 <!-- Test with Psl --> |
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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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155 <test> |
|
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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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|
156 <param name="genome_name" value="Dbia3"/> |
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7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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157 <param name="fasta_file" value="common/dbia3.fa"/> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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158 <repeat name="group"> |
|
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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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|
159 <param name="group_name" value="Default group"/> |
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7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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160 <repeat name="format"> |
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161 <conditional name="formatChoice"> |
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162 <param name="format_select" value="psl"/> |
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163 <param name="PSL" value="psl/inputs/blastXmlToPsl"/> |
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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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164 <param name="longLabel" value="BLAST Alignment" /> |
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165 <param name="track_color" value="#000000"/> |
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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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166 </conditional> |
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167 </repeat> |
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168 </repeat> |
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169 <output name="output" file="psl/psl_trackhub.html"> |
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170 <extra_files type="file" |
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171 name="myHub/Dbia3/tracks/blastXmlToPsl.bb" |
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172 value="psl/myHub/Dbia3/tracks/blastXmlToPsl.bb" |
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173 compare="sim_size" |
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174 /> |
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175 <expand macro="verify_hub_structure" test="psl" /> |
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176 </output> |
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177 </test> |
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178 |
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179 <!-- Test with BigWig --> |
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180 <test> |
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181 <param name="genome_name" value="Dbia3"/> |
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182 <param name="fasta_file" value="common/dbia3.fa"/> |
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183 <repeat name="group"> |
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184 <param name="group_name" value="Default group"/> |
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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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185 <repeat name="format"> |
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186 <conditional name="formatChoice"> |
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187 <param name="format_select" value="bigwig"/> |
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188 <param name="BIGWIG" value="bigwig/inputs/RNA-Seq_Alignment_Coverage"/> |
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189 <param name="longLabel" value="RNA-Seq Coverage" /> |
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190 <param name="track_color" value="#000000"/> |
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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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191 </conditional> |
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192 </repeat> |
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193 </repeat> |
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194 <output name="output" file="bigwig/bigwig.html"> |
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195 <extra_files type="file" |
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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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196 name="myHub/Dbia3/tracks/RNA-Seq_Alignment_Coverage.bigwig" |
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197 value="bigwig/myHub/Dbia3/tracks/RNA-Seq_Alignment_Coverage.bigwig" |
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198 compare="sim_size" |
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199 /> |
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200 <expand macro="verify_hub_structure" test="bigwig" /> |
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201 <!-- check additional trackDb settings for BigWig --> |
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202 <extra_files type="file" name="myHub/Dbia3/trackDb.txt"> |
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203 <assert_contents> |
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204 <has_text text="autoScale"/> |
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205 <has_text text="maxHeightPixels"/> |
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206 <has_text text="windowingFunction"/> |
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207 </assert_contents> |
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208 </extra_files> |
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209 </output> |
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210 </test> |
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211 |
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212 <!-- Test with GFF3 --> |
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213 <test> |
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214 <param name="genome_name" value="Dbia3"/> |
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215 <param name="fasta_file" value="common/dbia3.fa"/> |
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216 <repeat name="group"> |
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217 <param name="group_name" value="Default group"/> |
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218 <repeat name="format"> |
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219 <conditional name="formatChoice"> |
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220 <param name="format_select" value="gff3"/> |
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221 <param name="GFF3" value="gff3/inputs/Augustus_Gene_Predictions"/> |
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222 <param name="longLabel" value="Augustus" /> |
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223 <param name="track_color" value="#000000"/> |
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224 </conditional> |
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225 </repeat> |
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226 </repeat> |
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227 <output name="output" file="gff3/gff3_trackhub.html"> |
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228 <extra_files type="file" |
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229 name="myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb" |
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230 value="gff3/myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb" |
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231 compare="sim_size" |
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232 /> |
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233 <expand macro="verify_hub_structure" test="gff3" /> |
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234 </output> |
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235 </test> |
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236 |
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237 <!-- Test with GTF --> |
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238 <test> |
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239 <param name="genome_name" value="Dbia3"/> |
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240 <param name="fasta_file" value="common/dbia3.fa"/> |
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241 <repeat name="group"> |
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242 <param name="group_name" value="Default group"/> |
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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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243 <repeat name="format"> |
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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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244 <conditional name="formatChoice"> |
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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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245 <param name="format_select" value="gtf"/> |
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7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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246 <param name="GTF" value="gtf/inputs/StringTie_Assembled_Transcripts"/> |
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247 <param name="longLabel" value="StringTie transcripts" /> |
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248 <param name="track_color" value="#000000"/> |
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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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249 </conditional> |
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250 </repeat> |
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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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251 </repeat> |
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252 <output name="output" file="gtf/gtf_trackhub.html"> |
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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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253 <extra_files type="file" |
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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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254 name="myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb" |
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7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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255 value="gtf/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb" |
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256 compare="sim_size" |
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7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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257 /> |
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258 <expand macro="verify_hub_structure" test="gtf" /> |
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259 </output> |
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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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260 </test> |
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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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261 |
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262 <!-- Test with BLAT Alignment --> |
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263 <test> |
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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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264 <param name="genome_name" value="Dbia3"/> |
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7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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265 <param name="fasta_file" value="common/dbia3.fa"/> |
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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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266 <repeat name="group"> |
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267 <param name="group_name" value="Default group"/> |
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268 <repeat name="format"> |
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269 <conditional name="formatChoice"> |
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270 <param name="format_select" value="bed" /> |
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271 <conditional name="bedChoice"> |
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272 <param name="bed_select" value="bed_blat_alignment_option"/> |
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273 <param name="BED_blat_alignment" ftype="bed" value="bed_blat_alignment/inputs/BLAT_alignment_bigpsl"/> |
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274 <param name="longLabel" value="BLAT alignment" /> |
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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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275 <param name="track_color" value="#000000"/> |
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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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276 <param name="database" value="NCBI" /> |
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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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277 </conditional> |
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278 </conditional> |
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279 </repeat> |
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280 </repeat> |
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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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281 <output name="output" file="bed_blat_alignment/blat_alignment_trackhub.html"> |
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282 <extra_files type="file" |
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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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283 name="myHub/Dbia3/tracks/BLAT_alignment_bigpsl.bb" |
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7e8a8b732db3
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284 value="bed_blat_alignment/myHub/Dbia3/tracks/BLAT_alignment_bigpsl.bb" |
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285 compare="sim_size" |
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7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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286 /> |
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287 <expand macro="verify_hub_structure" test="bed_blat_alignment" /> |
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288 <!-- check additional trackDb settings for BLAT --> |
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289 <extra_files type="file" name="myHub/Dbia3/trackDb.txt"> |
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290 <assert_contents> |
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291 <has_text text="searchIndex"/> |
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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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292 <has_text text="url"/> |
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293 <has_text text="urlLabel"/> |
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294 <has_text text="iframeUrl"/> |
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295 <has_text text="iframeOptions"/> |
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296 </assert_contents> |
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297 </extra_files> |
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298 </output> |
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299 </test> |
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300 |
|
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301 <!-- Test with BLAST Alignment --> |
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302 <test> |
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303 <param name="genome_name" value="Dbia3"/> |
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304 <param name="fasta_file" value="common/dbia3.fa"/> |
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305 <repeat name="group"> |
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306 <param name="group_name" value="Default group"/> |
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307 <repeat name="format"> |
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308 <conditional name="formatChoice"> |
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309 <param name="format_select" value="bed" /> |
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310 <conditional name="bedChoice"> |
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311 <param name="bed_select" value="bed_blast_alignment_option"/> |
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312 <param name="BED_blast_alignment" ftype="bed" value="bed_blast_alignment/inputs/BLAST_alignment_bigpsl"/> |
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313 <param name="longLabel" value="BLAST alignment" /> |
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314 <param name="track_color" value="#000000"/> |
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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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315 <param name="database" value="NCBI" /> |
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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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316 </conditional> |
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317 </conditional> |
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318 </repeat> |
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319 </repeat> |
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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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320 <output name="output" file="bed_blast_alignment/blast_alignment_trackhub.html"> |
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321 <extra_files type="file" |
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322 name="myHub/Dbia3/tracks/BLAST_alignment_bigpsl.bb" |
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323 value="bed_blast_alignment/myHub/Dbia3/tracks/BLAST_alignment_bigpsl.bb" |
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324 compare="sim_size" |
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|
325 /> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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|
326 <expand macro="verify_hub_structure" test="bed_blast_alignment" /> |
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7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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|
327 <!-- check additional trackDb settings for BLAST --> |
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7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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|
328 <extra_files type="file" name="myHub/Dbia3/trackDb.txt"> |
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7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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|
329 <assert_contents> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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|
330 <has_text text="searchIndex"/> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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|
331 <has_text text="url"/> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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|
332 <has_text text="urlLabel"/> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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|
333 <has_text text="iframeUrl"/> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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parents:
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|
334 <has_text text="iframeOptions"/> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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|
335 </assert_contents> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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|
336 </extra_files> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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|
337 </output> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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|
338 </test> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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parents:
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|
339 |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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changeset
|
340 <!-- Test with Regtools Splice Junctions --> |
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7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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parents:
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|
341 <test> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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|
342 <param name="genome_name" value="Dbia3"/> |
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7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
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|
343 <param name="fasta_file" value="common/dbia3.fa"/> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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|
344 <repeat name="group"> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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parents:
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|
345 <param name="group_name" value="Default group"/> |
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7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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|
346 <repeat name="format"> |
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7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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parents:
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changeset
|
347 <conditional name="formatChoice"> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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parents:
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|
348 <param name="format_select" value="bed" /> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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parents:
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|
349 <conditional name="bedChoice"> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
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changeset
|
350 <param name="bed_select" value="bed_splice_junctions_option"/> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
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changeset
|
351 <param name="BED_splice_junctions" ftype="bed" value="bed_splice_junctions/inputs/regtools_junctions"/> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
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|
352 <param name="longLabel" value="Splice junctions" /> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
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|
353 <param name="track_color" value="#000000"/> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
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|
354 </conditional> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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parents:
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|
355 </conditional> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
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changeset
|
356 </repeat> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
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changeset
|
357 </repeat> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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parents:
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changeset
|
358 <output name="output" file="bed_splice_junctions/splice_junctions_trackhub.html"> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
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|
359 <extra_files type="file" |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
360 name="myHub/Dbia3/tracks/regtools_junctions.bb" |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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parents:
diff
changeset
|
361 value="bed_splice_junctions/myHub/Dbia3/tracks/regtools_junctions.bb" |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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parents:
diff
changeset
|
362 compare="sim_size" |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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|
363 /> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
364 <expand macro="verify_hub_structure" test="bed_splice_junctions" /> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
365 </output> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
366 </test> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
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changeset
|
367 |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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parents:
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changeset
|
368 <!-- Test with Cytoband --> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
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changeset
|
369 <test> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
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changeset
|
370 <param name="genome_name" value="Dbia3"/> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
371 <param name="fasta_file" value="common/dbia3.fa"/> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
372 <repeat name="group"> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
373 <param name="group_name" value="Default group"/> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
374 <repeat name="format"> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
375 <conditional name="formatChoice"> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
376 <param name="format_select" value="bed" /> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
377 <conditional name="bedChoice"> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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parents:
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changeset
|
378 <param name="bed_select" value="bed_cytoBand"/> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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parents:
diff
changeset
|
379 <param name="BED_cytoBand" ftype="bed" value="bed_cytoband/inputs/Cytoband"/> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
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changeset
|
380 <param name="longLabel" value="Cytoband" /> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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parents:
diff
changeset
|
381 <param name="track_color" value="#000000"/> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
382 </conditional> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
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changeset
|
383 </conditional> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
384 </repeat> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
385 </repeat> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
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changeset
|
386 <output name="output" file="bed_cytoband/cytoband_trackhub.html"> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
387 <extra_files type="file" |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
388 name="myHub/Dbia3/tracks/Cytoband.bb" |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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parents:
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changeset
|
389 value="bed_cytoband/myHub/Dbia3/tracks/Cytoband.bb" |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
390 compare="sim_size" |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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parents:
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changeset
|
391 /> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
392 <expand macro="verify_hub_structure" test="bed_cytoband" /> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
393 <extra_files type="file" name="myHub/Dbia3/trackDb.txt"> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
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parents:
diff
changeset
|
394 <assert_contents> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
395 <has_text text="track cytoBandIdeo"/> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
396 </assert_contents> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
397 </extra_files> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
398 </output> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
399 </test> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
400 |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
401 <!-- Test with bigBed --> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
402 <test> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
403 <param name="genome_name" value="Dbia3"/> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
404 <param name="fasta_file" value="common/dbia3.fa"/> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
405 <repeat name="group"> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
406 <param name="group_name" value="Default group"/> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
407 <repeat name="format"> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
408 <conditional name="formatChoice"> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
409 <param name="format_select" value="bigbed"/> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
410 <param name="BIGBED" value="big_bed/inputs/BLAT_alignment_bigbed" /> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
411 <param name="longLabel" value="bigBed" /> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
412 <param name="track_color" value="#000000"/> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
413 </conditional> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
414 </repeat> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
415 </repeat> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
416 <output name="output" file="big_bed/bigbed_trackhub.html"> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
417 <extra_files type="file" |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
418 name="myHub/Dbia3/tracks/BLAT_alignment_bigbed.bigbed" |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
419 value="big_bed/myHub/Dbia3/tracks/BLAT_alignment_bigbed.bigbed" |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
420 compare="sim_size" |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
421 /> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
422 <expand macro="verify_hub_structure" test="big_bed" /> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
423 </output> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
424 </test> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
425 |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
426 <!-- Test with one group and multiple tracks --> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
427 <test> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
428 <param name="genome_name" value="Dbia3"/> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
429 <param name="fasta_file" value="common/dbia3.fa"/> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
430 <repeat name="group"> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
431 <param name="group_name" value="Default group"/> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
432 <repeat name="format"> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
433 <conditional name="formatChoice"> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
434 <param name="format_select" value="gtf"/> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
435 <param name="GTF" value="gtf/inputs/StringTie_Assembled_Transcripts"/> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
436 <param name="track_color" value="#000000"/> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
437 </conditional> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
438 </repeat> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
439 <repeat name="format"> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
440 <conditional name="formatChoice"> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
441 <param name="format_select" value="gff3"/> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
442 <param name="GFF3" value="gff3/inputs/Augustus_Gene_Predictions"/> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
443 <param name="track_color" value="#000000"/> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
444 </conditional> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
445 </repeat> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
446 </repeat> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
447 <output name="output" file="gtf_gff/gtf_gff_trackhub.html"> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
448 <extra_files type="file" |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
449 name="myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb" |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
450 value="gtf/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb" |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
451 compare="sim_size" |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
452 /> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
453 <extra_files type="file" |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
454 name="myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb" |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
455 value="gff3/myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb" |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
456 compare="sim_size" |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
457 /> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
458 <expand macro="verify_hub_structure" test="gtf_gff" /> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
459 </output> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
460 </test> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
461 |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
462 <!-- Test with one group and all the supported datatypes --> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
463 <test> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
464 <param name="genome_name" value="Dbia3"/> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
465 <param name="fasta_file" value="common/dbia3.fa"/> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
466 <repeat name="group"> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
467 <param name="group_name" value="Default group"/> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
468 <repeat name="format"> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
469 <conditional name="formatChoice"> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
470 <param name="format_select" value="bam"/> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
471 <param name="BAM" value="bam/inputs/HISAT2_Accepted_Hits.bam"/> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
472 <param name="track_color" value="#000000"/> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
473 </conditional> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
474 </repeat> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
475 <repeat name="format"> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
476 <conditional name="formatChoice"> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
477 <param name="format_select" value="bed"/> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
478 <conditional name="bedChoice"> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
479 <param name="bed_select" value="bed_generic"/> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
480 <param name="BED" ftype="bed" value="bed_generic/inputs/TBLASTN_Alignment_to_proteins"/> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
481 <param name="track_color" value="#000000"/> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
482 </conditional> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
483 </conditional> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
484 </repeat> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
485 <repeat name="format"> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
486 <conditional name="formatChoice"> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
487 <param name="format_select" value="bed"/> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
488 <conditional name="bedChoice"> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
489 <param name="bed_select" value="bed_simple_repeats_option"/> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
490 <param name="BED_simple_repeats" ftype="bed" |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
491 value="bed_simple_repeats/inputs/Repeating_Elements_by_TrfBig"/> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
492 <param name="track_color" value="#000000"/> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
493 </conditional> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
494 </conditional> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
495 </repeat> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
496 <repeat name="format"> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
497 <conditional name="formatChoice"> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
498 <param name="format_select" value="psl"/> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
499 <param name="PSL" value="psl/inputs/blastXmlToPsl"/> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
500 <param name="track_color" value="#000000"/> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
501 </conditional> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
502 </repeat> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
503 <repeat name="format"> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
504 <conditional name="formatChoice"> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
505 <param name="format_select" value="bigwig"/> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
506 <param name="BIGWIG" value="bigwig/inputs/RNA-Seq_Alignment_Coverage"/> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
507 <param name="track_color" value="#000000"/> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
508 </conditional> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
509 </repeat> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
510 <repeat name="format"> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
511 <conditional name="formatChoice"> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
512 <param name="format_select" value="gff3"/> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
513 <param name="GFF3" value="gff3/inputs/Augustus_Gene_Predictions"/> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
514 <param name="track_color" value="#000000"/> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
515 </conditional> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
516 </repeat> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
517 <repeat name="format"> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
518 <conditional name="formatChoice"> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
519 <param name="format_select" value="gtf"/> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
520 <param name="GTF" value="gtf/inputs/StringTie_Assembled_Transcripts"/> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
521 <param name="track_color" value="#000000"/> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
522 </conditional> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
523 </repeat> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
524 <repeat name="format"> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
525 <conditional name="formatChoice"> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
526 <param name="format_select" value="bed" /> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
527 <conditional name="bedChoice"> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
528 <param name="bed_select" value="bed_cytoBand"/> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
529 <param name="BED_cytoBand" ftype="bed" value="bed_cytoband/inputs/Cytoband"/> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
530 <param name="track_color" value="#000000"/> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
531 </conditional> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
532 </conditional> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
533 </repeat> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
534 <repeat name="format"> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
535 <conditional name="formatChoice"> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
536 <param name="format_select" value="bed" /> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
537 <conditional name="bedChoice"> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
538 <param name="bed_select" value="bed_splice_junctions_option"/> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
539 <param name="BED_splice_junctions" ftype="bed" value="bed_splice_junctions/inputs/regtools_junctions"/> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
540 <param name="track_color" value="#000000"/> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
541 </conditional> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
542 </conditional> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
543 </repeat> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
544 <repeat name="format"> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
545 <conditional name="formatChoice"> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
546 <param name="format_select" value="bed" /> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
547 <conditional name="bedChoice"> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
548 <param name="bed_select" value="bed_blast_alignment_option"/> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
549 <param name="BED_blast_alignment" ftype="bed" value="bed_blast_alignment/inputs/BLAST_alignment_bigpsl"/> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
550 <param name="track_color" value="#000000"/> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
551 <param name="database" value="NCBI" /> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
552 </conditional> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
553 </conditional> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
554 </repeat> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
555 <repeat name="format"> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
556 <conditional name="formatChoice"> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
557 <param name="format_select" value="bed" /> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
558 <conditional name="bedChoice"> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
559 <param name="bed_select" value="bed_blat_alignment_option"/> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
560 <param name="BED_blat_alignment" ftype="bed" value="bed_blat_alignment/inputs/BLAT_alignment_bigpsl"/> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
561 <param name="track_color" value="#000000"/> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
562 <param name="database" value="NCBI" /> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
563 </conditional> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
564 </conditional> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
565 </repeat> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
566 </repeat> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
567 <output name="output" file="all_datatypes/all_datatypes_trackhub.html"> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
568 <!-- verify tracks folder contains all the files --> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
569 <extra_files type="file" |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
570 name="myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam" |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
571 value="all_datatypes/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam" |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
572 compare="sim_size" |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
573 /> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
574 <extra_files type="file" |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
575 name="myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai" |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
576 value="all_datatypes/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai" |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
577 compare="sim_size" |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
578 /> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
579 <extra_files type="file" |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
580 name="myHub/Dbia3/tracks/TBLASTN_Alignment_to_proteins.bb" |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
581 value="all_datatypes/myHub/Dbia3/tracks/TBLASTN_Alignment_to_proteins.bb" |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
582 compare="sim_size" |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
583 /> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
584 <extra_files type="file" |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
585 name="myHub/Dbia3/tracks/Repeating_Elements_by_TrfBig.bb" |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
586 value="all_datatypes/myHub/Dbia3/tracks/Repeating_Elements_by_TrfBig.bb" |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
587 compare="sim_size" |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
588 /> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
589 <extra_files type="file" |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
590 name="myHub/Dbia3/tracks/blastXmlToPsl.bb" |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
591 value="all_datatypes/myHub/Dbia3/tracks/blastXmlToPsl.bb" |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
592 compare="sim_size" |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
593 /> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
594 <extra_files type="file" |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
595 name="myHub/Dbia3/tracks/RNA-Seq_Alignment_Coverage.bigwig" |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
596 value="all_datatypes/myHub/Dbia3/tracks/RNA-Seq_Alignment_Coverage.bigwig" |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
597 compare="sim_size" |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
598 /> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
599 <extra_files type="file" |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
600 name="myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb" |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
601 value="all_datatypes/myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb" |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
602 compare="sim_size" |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
603 /> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
604 <extra_files type="file" |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
605 name="myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb" |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
606 value="all_datatypes/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb" |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
607 compare="sim_size" |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
608 /> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
609 <extra_files type="file" |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
610 name="myHub/Dbia3/tracks/Cytoband.bb" |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
611 value="all_datatypes/myHub/Dbia3/tracks/Cytoband.bb" |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
612 compare="sim_size" |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
613 /> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
614 <extra_files type="file" |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
615 name="myHub/Dbia3/tracks/regtools_junctions.bb" |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
616 value="all_datatypes/myHub/Dbia3/tracks/regtools_junctions.bb" |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
617 compare="sim_size" |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
618 /> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
619 <extra_files type="file" |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
620 name="myHub/Dbia3/tracks/BLAST_alignment_bigpsl.bb" |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
621 value="all_datatypes/myHub/Dbia3/tracks/BLAST_alignment_bigpsl.bb" |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
622 compare="sim_size" |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
623 /> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
624 <extra_files type="file" |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
625 name="myHub/Dbia3/tracks/BLAT_alignment_bigpsl.bb" |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
626 value="all_datatypes/myHub/Dbia3/tracks/BLAT_alignment_bigpsl.bb" |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
627 compare="sim_size" |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
628 /> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
629 <expand macro="verify_hub_structure" test="all_datatypes" /> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
630 </output> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
631 </test> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
632 |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
633 <!-- Test with two groups and no tracks --> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
634 <test> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
635 <param name="genome_name" value="Dbia3"/> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
636 <param name="fasta_file" value="common/dbia3.fa"/> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
637 <repeat name="group"> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
638 <param name="group_name" value="Default group"/> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
639 </repeat> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
640 <repeat name="group"> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
641 <param name="group_name" value="Other group"/> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
642 </repeat> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
643 <output name="output" file="two_groups_no_track/two_groups_no_track_trackhub.html"> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
644 <expand macro="verify_hub_structure_no_track" test="two_groups_no_track" /> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
645 </output> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
646 </test> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
647 |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
648 <!-- Test with two groups and one track in first --> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
649 <test> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
650 <param name="genome_name" value="Dbia3"/> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
651 <param name="fasta_file" value="common/dbia3.fa"/> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
652 <repeat name="group"> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
653 <param name="group_name" value="Default group"/> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
654 <repeat name="format"> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
655 <conditional name="formatChoice"> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
656 <param name="format_select" value="bigwig"/> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
657 <param name="BIGWIG" value="bigwig/inputs/RNA-Seq_Alignment_Coverage"/> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
658 <param name="track_color" value="#000000"/> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
659 </conditional> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
660 </repeat> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
661 </repeat> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
662 <repeat name="group"> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
663 <param name="group_name" value="Other group"/> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
664 </repeat> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
665 <output name="output" file="two_groups_one_track_first/two_groups_one_track_first_trackhub.html"> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
666 <!-- Check tracks exist --> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
667 <extra_files type="file" |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
668 name="myHub/Dbia3/tracks/RNA-Seq_Alignment_Coverage.bigwig" |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
669 value="bigwig/myHub/Dbia3/tracks/RNA-Seq_Alignment_Coverage.bigwig" |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
670 compare="sim_size" |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
671 /> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
672 <expand macro="verify_hub_structure" test="two_groups_one_track_first" /> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
673 </output> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
674 </test> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
675 |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
676 <!-- Test with two groups and one track in both --> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
677 <test> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
678 <param name="genome_name" value="Dbia3"/> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
679 <param name="fasta_file" value="common/dbia3.fa"/> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
680 <repeat name="group"> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
681 <param name="group_name" value="Default group"/> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
682 <repeat name="format"> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
683 <conditional name="formatChoice"> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
684 <param name="format_select" value="bigwig"/> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
685 <param name="BIGWIG" value="bigwig/inputs/RNA-Seq_Alignment_Coverage"/> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
686 <param name="track_color" value="#000000"/> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
687 </conditional> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
688 </repeat> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
689 </repeat> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
690 <repeat name="group"> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
691 <param name="group_name" value="Other group"/> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
692 <repeat name="format"> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
693 <conditional name="formatChoice"> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
694 <param name="format_select" value="gtf"/> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
695 <param name="GTF" value="gtf/inputs/StringTie_Assembled_Transcripts"/> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
696 <param name="track_color" value="#000000"/> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
697 </conditional> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
698 </repeat> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
699 </repeat> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
700 <output name="output" file="two_groups_one_track_both/two_groups_one_track_both_trackhub.html"> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
701 <!-- Check tracks exist --> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
702 <!-- First group --> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
703 <extra_files type="file" |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
704 name="myHub/Dbia3/tracks/RNA-Seq_Alignment_Coverage.bigwig" |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
705 value="bigwig/myHub/Dbia3/tracks/RNA-Seq_Alignment_Coverage.bigwig" |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
706 compare="sim_size" |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
707 /> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
708 |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
709 <!-- Second group --> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
710 <extra_files type="file" |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
711 name="myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb" |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
712 value="gtf/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb" |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
713 compare="sim_size" |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
714 /> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
715 <expand macro="verify_hub_structure" test="two_groups_one_track_both" /> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
716 <!-- Check the groups.txt exists and is properly populated --> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
717 </output> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
718 </test> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
719 |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
720 <!-- Test with two groups and multiple tracks in both --> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
721 <test> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
722 <param name="genome_name" value="Dbia3"/> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
723 <param name="fasta_file" value="common/dbia3.fa"/> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
724 <repeat name="group"> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
725 <param name="group_name" value="Default group"/> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
726 <repeat name="format"> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
727 <conditional name="formatChoice"> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
728 <param name="format_select" value="bigwig"/> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
729 <param name="BIGWIG" value="bigwig/inputs/RNA-Seq_Alignment_Coverage"/> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
730 <param name="track_color" value="#000000"/> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
731 </conditional> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
732 </repeat> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
733 <repeat name="format"> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
734 <conditional name="formatChoice"> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
735 <param name="format_select" value="bam"/> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
736 <param name="BAM" value="bam/inputs/HISAT2_Accepted_Hits.bam"/> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
737 <param name="track_color" value="#000000"/> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
738 </conditional> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
739 </repeat> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
740 </repeat> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
741 <repeat name="group"> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
742 <param name="group_name" value="Other group"/> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
743 <repeat name="format"> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
744 <conditional name="formatChoice"> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
745 <param name="format_select" value="gtf"/> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
746 <param name="GTF" value="gtf/inputs/StringTie_Assembled_Transcripts"/> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
747 <param name="track_color" value="#000000"/> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
748 </conditional> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
749 </repeat> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
750 <repeat name="format"> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
751 <conditional name="formatChoice"> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
752 <param name="format_select" value="gff3"/> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
753 <param name="GFF3" value="gff3_multi_fasta/inputs/Multi-Fasta_GlimmerHMM_Gene_Predictions"/> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
754 <param name="track_color" value="#000000"/> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
755 </conditional> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
756 </repeat> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
757 </repeat> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
758 <output name="output" file="two_groups_multiple_tracks/two_groups_multiple_tracks_trackhub.html"> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
759 <!-- Check tracks exist --> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
760 <!-- First group --> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
761 <extra_files type="file" |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
762 name="myHub/Dbia3/tracks/RNA-Seq_Alignment_Coverage.bigwig" |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
763 value="bigwig/myHub/Dbia3/tracks/RNA-Seq_Alignment_Coverage.bigwig" |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
764 compare="sim_size" |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
765 /> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
766 <extra_files type="file" |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
767 name="myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam" |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
768 value="bam/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam" |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
769 compare="sim_size" |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
770 /> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
771 <extra_files type="file" |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
772 name="myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai" |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
773 value="bam/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai" |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
774 compare="sim_size" |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
775 /> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
776 |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
777 <!-- Second group --> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
778 <extra_files type="file" |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
779 name="myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb" |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
780 value="gtf/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb" |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
781 compare="sim_size" |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
782 /> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
783 <extra_files type="file" |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
784 name="myHub/Dbia3/tracks/Multi-Fasta_GlimmerHMM_Gene_Predictions.bb" |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
785 value="gff3_multi_fasta/myHub/Dbia3/tracks/Multi-Fasta_GlimmerHMM_Gene_Predictions.bb" |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
786 compare="sim_size" |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
787 /> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
788 <expand macro="verify_hub_structure" test="two_groups_multiple_tracks" /> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
789 </output> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
790 </test> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
791 |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
792 <!-- Test default color in a track --> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
793 <test> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
794 <param name="genome_name" value="Dbia3"/> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
795 <param name="fasta_file" value="common/dbia3.fa"/> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
796 <repeat name="group"> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
797 <param name="group_name" value="Default group"/> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
798 <repeat name="format"> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
799 <conditional name="formatChoice"> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
800 <param name="format_select" value="bam"/> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
801 <param name="BAM" value="bam/inputs/HISAT2_Accepted_Hits.bam"/> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
802 <param name="track_color" value="#000000"/> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
803 </conditional> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
804 </repeat> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
805 </repeat> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
806 <output name="output" file="default_color/default_color_trackhub.html"> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
807 <expand macro="verify_hub_structure" test="default_color" /> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
808 <!-- Verify trackDb.txt contains the color 0,0,0 --> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
809 <extra_files type="file" name="myHub/Dbia3/trackDb.txt"> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
810 <assert_contents> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
811 <has_text text="color 0,0,0"/> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
812 </assert_contents> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
813 </extra_files> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
814 |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
815 <!-- TODO: Find a way to check also that the whole common structure is intact too, without too much repetition --> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
816 </output> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
817 </test> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
818 |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
819 <!-- Test changed color in a track --> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
820 <test> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
821 <param name="genome_name" value="Dbia3"/> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
822 <param name="fasta_file" value="common/dbia3.fa"/> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
823 <repeat name="group"> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
824 <param name="group_name" value="Default group"/> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
825 <repeat name="format"> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
826 <conditional name="formatChoice"> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
827 <param name="format_select" value="bam"/> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
828 <param name="BAM" value="bam/inputs/HISAT2_Accepted_Hits.bam"/> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
829 <param name="track_color" value="#8064a2"/> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
830 </conditional> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
831 </repeat> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
832 </repeat> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
833 <output name="output" file="changed_color/changed_color_trackhub.html"> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
834 <expand macro="verify_hub_structure" test="changed_color" /> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
835 <!-- Verify trackDb.txt contains the color 128,100,162 --> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
836 <extra_files type="file" name="myHub/Dbia3/trackDb.txt"> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
837 <assert_contents> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
838 <has_text text="color 128,100,162"/> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
839 </assert_contents> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
840 </extra_files> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
841 |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
842 <!-- TODO: Find a way to check also that the whole common structure is intact too, without too much repetition --> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
843 </output> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
844 </test> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
845 |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
846 <!-- Test for StringTie Chromosome end coordinates --> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
847 <test> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
848 <param name="genome_name" value="Dbia3"/> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
849 <param name="fasta_file" value="common/dbia3.fa"/> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
850 <repeat name="group"> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
851 <param name="group_name" value="Default group"/> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
852 <repeat name="format"> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
853 <conditional name="formatChoice"> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
854 <param name="format_select" value="gtf"/> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
855 <param name="GTF" ftype="gtf" value="stringtie_chromosome_end_coordinates/inputs/StringTie_Assembled_Transcripts"/> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
856 <param name="track_color" value="#000000"/> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
857 </conditional> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
858 </repeat> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
859 </repeat> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
860 <output name="output" file="stringtie_chromosome_end_coordinates/stringtie_chromosome_end_coordinates_trackhub.html"> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
861 <extra_files type="file" |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
862 name="myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb" |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
863 value="stringtie_chromosome_end_coordinates/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb" |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
864 compare="sim_size" |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
865 /> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
866 <expand macro="verify_hub_structure" test="stringtie_chromosome_end_coordinates" /> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
867 |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
868 <!-- TODO: Find a way to check also that the whole common structure is intact too, without too much repetition --> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
869 </output> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
870 </test> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
871 |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
872 <!-- Test default label in a track --> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
873 <test> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
874 <param name="genome_name" value="Dbia3"/> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
875 <param name="fasta_file" value="common/dbia3.fa"/> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
876 <repeat name="group"> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
877 <param name="group_name" value="Default group"/> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
878 <repeat name="format"> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
879 <conditional name="formatChoice"> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
880 <param name="format_select" value="bam"/> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
881 <param name="BAM" value="bam/inputs/HISAT2_Accepted_Hits.bam"/> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
882 <param name="track_color" value="#000000"/> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
883 </conditional> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
884 </repeat> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
885 </repeat> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
886 <output name="output" file="default_color/default_color_trackhub.html"> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
887 <expand macro="verify_hub_structure" test="default_color" /> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
888 <!-- Verify trackDb.txt contains default label --> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
889 <extra_files type="file" name="myHub/Dbia3/trackDb.txt"> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
890 <assert_contents> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
891 <has_text text="longLabel HISAT2 Accepted Hits.bam"/> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
892 </assert_contents> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
893 </extra_files> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
894 |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
895 <!-- TODO: Find a way to check also that the whole common structure is intact too, without too much repetition --> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
896 </output> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
897 </test> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
898 |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
899 <!-- Test customized label in a track --> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
900 <test> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
901 <param name="genome_name" value="Dbia3"/> |
|
7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
|
902 <param name="fasta_file" value="common/dbia3.fa"/> |
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7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
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903 <repeat name="group"> |
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7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
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904 <param name="group_name" value="Default group"/> |
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7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
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905 <repeat name="format"> |
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7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
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906 <conditional name="formatChoice"> |
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7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
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907 <param name="format_select" value="bam"/> |
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7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
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908 <param name="BAM" value="bam/inputs/HISAT2_Accepted_Hits.bam"/> |
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7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
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909 <param name="longLabel" value="HISAT sequence alignment" /> |
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7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
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910 <param name="track_color" value="#000000"/> |
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7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
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changeset
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911 </conditional> |
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7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
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912 </repeat> |
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7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
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913 </repeat> |
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7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
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914 <output name="output" file="changed_label/changed_label_trackhub.html"> |
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7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
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changeset
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915 <expand macro="verify_hub_structure" test="changed_label" /> |
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7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
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916 <!-- Verify trackDb.txt contains the customized label --> |
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7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
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917 <extra_files type="file" name="myHub/Dbia3/trackDb.txt"> |
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7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
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changeset
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918 <assert_contents> |
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7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
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changeset
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919 <has_text text="longLabel HISAT sequence alignment"/> |
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7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
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changeset
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920 </assert_contents> |
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7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
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921 </extra_files> |
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7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
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changeset
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922 |
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7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
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923 <!-- TODO: Find a way to check also that the whole common structure is intact too, without too much repetition --> |
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7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
diff
changeset
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924 </output> |
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7e8a8b732db3
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
yating-l
parents:
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925 </test> |