Mercurial > repos > iuc > export2graphlan
annotate export2graphlan.xml @ 2:635c90a27692 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 1a2cbe050c6b172147064cb53b16d6833f138b68
author | iuc |
---|---|
date | Fri, 09 Feb 2024 21:29:27 +0000 |
parents | b16989c1e3a7 |
children |
rev | line source |
---|---|
1
b16989c1e3a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 457ccc12f14e041fe6dd7ca2a7e46a0237df4a21
iuc
parents:
0
diff
changeset
|
1 <tool id="export2graphlan" name="Export to GraPhlAn" version="@VERSION@+@GALAXY_VERSION@"> |
b16989c1e3a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 457ccc12f14e041fe6dd7ca2a7e46a0237df4a21
iuc
parents:
0
diff
changeset
|
2 <macros> |
b16989c1e3a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 457ccc12f14e041fe6dd7ca2a7e46a0237df4a21
iuc
parents:
0
diff
changeset
|
3 <token name="@VERSION@">0.20</token> |
b16989c1e3a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 457ccc12f14e041fe6dd7ca2a7e46a0237df4a21
iuc
parents:
0
diff
changeset
|
4 <token name="@GALAXY_VERSION@">galaxy0</token> |
b16989c1e3a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 457ccc12f14e041fe6dd7ca2a7e46a0237df4a21
iuc
parents:
0
diff
changeset
|
5 </macros> |
2
635c90a27692
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 1a2cbe050c6b172147064cb53b16d6833f138b68
iuc
parents:
1
diff
changeset
|
6 <xrefs> |
635c90a27692
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 1a2cbe050c6b172147064cb53b16d6833f138b68
iuc
parents:
1
diff
changeset
|
7 <xref type="bio.tools">export2graphlan</xref> |
635c90a27692
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 1a2cbe050c6b172147064cb53b16d6833f138b68
iuc
parents:
1
diff
changeset
|
8 </xrefs> |
0
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
parents:
diff
changeset
|
9 <requirements> |
1
b16989c1e3a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 457ccc12f14e041fe6dd7ca2a7e46a0237df4a21
iuc
parents:
0
diff
changeset
|
10 <requirement type="package" version="@VERSION@">export2graphlan</requirement> |
0
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
parents:
diff
changeset
|
11 </requirements> |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
parents:
diff
changeset
|
12 <version_command> |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
parents:
diff
changeset
|
13 <![CDATA[ |
1
b16989c1e3a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 457ccc12f14e041fe6dd7ca2a7e46a0237df4a21
iuc
parents:
0
diff
changeset
|
14 export2graphlan.py -h | grep "ver." |
0
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
parents:
diff
changeset
|
15 ]]> |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
parents:
diff
changeset
|
16 </version_command> |
1
b16989c1e3a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 457ccc12f14e041fe6dd7ca2a7e46a0237df4a21
iuc
parents:
0
diff
changeset
|
17 <command detect_errors="exit_code"> |
0
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
parents:
diff
changeset
|
18 <![CDATA[ |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
parents:
diff
changeset
|
19 export2graphlan.py |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
parents:
diff
changeset
|
20 --lefse_input '$lefse_input' |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
parents:
diff
changeset
|
21 #if $input_lefse_output.input_lefse_output_test == "true" |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
parents:
diff
changeset
|
22 --lefse_output '$input_lefse_output.lefse_output' |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
parents:
diff
changeset
|
23 #end if |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
parents:
diff
changeset
|
24 -t '$tree' |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
parents:
diff
changeset
|
25 -a '$annotation' |
1
b16989c1e3a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 457ccc12f14e041fe6dd7ca2a7e46a0237df4a21
iuc
parents:
0
diff
changeset
|
26 #if str($annotations) != '' |
b16989c1e3a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 457ccc12f14e041fe6dd7ca2a7e46a0237df4a21
iuc
parents:
0
diff
changeset
|
27 --annotations $annotations |
0
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
parents:
diff
changeset
|
28 #end if |
1
b16989c1e3a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 457ccc12f14e041fe6dd7ca2a7e46a0237df4a21
iuc
parents:
0
diff
changeset
|
29 #if str($external_annotations) != '' |
b16989c1e3a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 457ccc12f14e041fe6dd7ca2a7e46a0237df4a21
iuc
parents:
0
diff
changeset
|
30 --external_annotations $external_annotations |
0
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
parents:
diff
changeset
|
31 #end if |
1
b16989c1e3a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 457ccc12f14e041fe6dd7ca2a7e46a0237df4a21
iuc
parents:
0
diff
changeset
|
32 #if str($background_levels) != '' |
b16989c1e3a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 457ccc12f14e041fe6dd7ca2a7e46a0237df4a21
iuc
parents:
0
diff
changeset
|
33 --background_levels $background_levels |
0
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
parents:
diff
changeset
|
34 #end if |
1
b16989c1e3a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 457ccc12f14e041fe6dd7ca2a7e46a0237df4a21
iuc
parents:
0
diff
changeset
|
35 #if str($background_clades) != '' |
0
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
parents:
diff
changeset
|
36 --background_clades '$background_clades' |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
parents:
diff
changeset
|
37 #end if |
1
b16989c1e3a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 457ccc12f14e041fe6dd7ca2a7e46a0237df4a21
iuc
parents:
0
diff
changeset
|
38 #if str($background_colors) != '' |
0
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
parents:
diff
changeset
|
39 --background_colors '$background_colors' |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
parents:
diff
changeset
|
40 #end if |
1
b16989c1e3a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 457ccc12f14e041fe6dd7ca2a7e46a0237df4a21
iuc
parents:
0
diff
changeset
|
41 #if str($title) != '' |
0
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
parents:
diff
changeset
|
42 --title '$title' |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
parents:
diff
changeset
|
43 #end if |
1
b16989c1e3a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 457ccc12f14e041fe6dd7ca2a7e46a0237df4a21
iuc
parents:
0
diff
changeset
|
44 #if str($title_font_size) != '' |
b16989c1e3a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 457ccc12f14e041fe6dd7ca2a7e46a0237df4a21
iuc
parents:
0
diff
changeset
|
45 --title_font_size $title_font_size |
b16989c1e3a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 457ccc12f14e041fe6dd7ca2a7e46a0237df4a21
iuc
parents:
0
diff
changeset
|
46 #end if |
b16989c1e3a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 457ccc12f14e041fe6dd7ca2a7e46a0237df4a21
iuc
parents:
0
diff
changeset
|
47 #if str($def_clade_size) != '' |
b16989c1e3a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 457ccc12f14e041fe6dd7ca2a7e46a0237df4a21
iuc
parents:
0
diff
changeset
|
48 --def_clade_size $def_clade_size |
b16989c1e3a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 457ccc12f14e041fe6dd7ca2a7e46a0237df4a21
iuc
parents:
0
diff
changeset
|
49 #end if |
b16989c1e3a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 457ccc12f14e041fe6dd7ca2a7e46a0237df4a21
iuc
parents:
0
diff
changeset
|
50 #if str($min_clade_size) != '' |
b16989c1e3a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 457ccc12f14e041fe6dd7ca2a7e46a0237df4a21
iuc
parents:
0
diff
changeset
|
51 --min_clade_size $min_clade_size |
b16989c1e3a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 457ccc12f14e041fe6dd7ca2a7e46a0237df4a21
iuc
parents:
0
diff
changeset
|
52 #end if |
b16989c1e3a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 457ccc12f14e041fe6dd7ca2a7e46a0237df4a21
iuc
parents:
0
diff
changeset
|
53 #if str($max_clade_size) != '' |
b16989c1e3a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 457ccc12f14e041fe6dd7ca2a7e46a0237df4a21
iuc
parents:
0
diff
changeset
|
54 --max_clade_size $max_clade_size |
0
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
parents:
diff
changeset
|
55 #end if |
1
b16989c1e3a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 457ccc12f14e041fe6dd7ca2a7e46a0237df4a21
iuc
parents:
0
diff
changeset
|
56 #if str($def_font_size) != '' |
b16989c1e3a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 457ccc12f14e041fe6dd7ca2a7e46a0237df4a21
iuc
parents:
0
diff
changeset
|
57 --def_font_size $def_font_size |
b16989c1e3a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 457ccc12f14e041fe6dd7ca2a7e46a0237df4a21
iuc
parents:
0
diff
changeset
|
58 #end if |
b16989c1e3a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 457ccc12f14e041fe6dd7ca2a7e46a0237df4a21
iuc
parents:
0
diff
changeset
|
59 #if str($min_font_size) != '' |
b16989c1e3a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 457ccc12f14e041fe6dd7ca2a7e46a0237df4a21
iuc
parents:
0
diff
changeset
|
60 --min_font_size $min_font_size |
b16989c1e3a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 457ccc12f14e041fe6dd7ca2a7e46a0237df4a21
iuc
parents:
0
diff
changeset
|
61 #end if |
b16989c1e3a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 457ccc12f14e041fe6dd7ca2a7e46a0237df4a21
iuc
parents:
0
diff
changeset
|
62 #if str($max_font_size) != '' |
b16989c1e3a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 457ccc12f14e041fe6dd7ca2a7e46a0237df4a21
iuc
parents:
0
diff
changeset
|
63 --max_font_size $max_font_size |
b16989c1e3a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 457ccc12f14e041fe6dd7ca2a7e46a0237df4a21
iuc
parents:
0
diff
changeset
|
64 #end if |
b16989c1e3a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 457ccc12f14e041fe6dd7ca2a7e46a0237df4a21
iuc
parents:
0
diff
changeset
|
65 #if str($annotation_legend_font_size) != '' |
b16989c1e3a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 457ccc12f14e041fe6dd7ca2a7e46a0237df4a21
iuc
parents:
0
diff
changeset
|
66 --annotation_legend_font_size $annotation_legend_font_size |
b16989c1e3a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 457ccc12f14e041fe6dd7ca2a7e46a0237df4a21
iuc
parents:
0
diff
changeset
|
67 #end if |
b16989c1e3a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 457ccc12f14e041fe6dd7ca2a7e46a0237df4a21
iuc
parents:
0
diff
changeset
|
68 #if str($abundance_threshold) != '' |
b16989c1e3a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 457ccc12f14e041fe6dd7ca2a7e46a0237df4a21
iuc
parents:
0
diff
changeset
|
69 --abundance_threshold $abundance_threshold |
0
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
parents:
diff
changeset
|
70 #end if |
1
b16989c1e3a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 457ccc12f14e041fe6dd7ca2a7e46a0237df4a21
iuc
parents:
0
diff
changeset
|
71 #if str($most_abundant) != '' |
b16989c1e3a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 457ccc12f14e041fe6dd7ca2a7e46a0237df4a21
iuc
parents:
0
diff
changeset
|
72 --most_abundant $most_abundant |
b16989c1e3a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 457ccc12f14e041fe6dd7ca2a7e46a0237df4a21
iuc
parents:
0
diff
changeset
|
73 #end if |
b16989c1e3a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 457ccc12f14e041fe6dd7ca2a7e46a0237df4a21
iuc
parents:
0
diff
changeset
|
74 #if str($least_biomarkers) != '' |
b16989c1e3a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 457ccc12f14e041fe6dd7ca2a7e46a0237df4a21
iuc
parents:
0
diff
changeset
|
75 --least_biomarkers $least_biomarkers |
0
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
parents:
diff
changeset
|
76 #end if |
1
b16989c1e3a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 457ccc12f14e041fe6dd7ca2a7e46a0237df4a21
iuc
parents:
0
diff
changeset
|
77 #if str($title_font_size) != '' |
b16989c1e3a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 457ccc12f14e041fe6dd7ca2a7e46a0237df4a21
iuc
parents:
0
diff
changeset
|
78 --fname_row $fname_row |
b16989c1e3a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 457ccc12f14e041fe6dd7ca2a7e46a0237df4a21
iuc
parents:
0
diff
changeset
|
79 #end if |
b16989c1e3a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 457ccc12f14e041fe6dd7ca2a7e46a0237df4a21
iuc
parents:
0
diff
changeset
|
80 #if str($title_font_size) != '' |
b16989c1e3a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 457ccc12f14e041fe6dd7ca2a7e46a0237df4a21
iuc
parents:
0
diff
changeset
|
81 --sname_row $sname_row |
b16989c1e3a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 457ccc12f14e041fe6dd7ca2a7e46a0237df4a21
iuc
parents:
0
diff
changeset
|
82 #end if |
b16989c1e3a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 457ccc12f14e041fe6dd7ca2a7e46a0237df4a21
iuc
parents:
0
diff
changeset
|
83 #if str($metadata_rows) != '' |
b16989c1e3a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 457ccc12f14e041fe6dd7ca2a7e46a0237df4a21
iuc
parents:
0
diff
changeset
|
84 --metadata_rows $metadata_rows |
0
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
parents:
diff
changeset
|
85 #end if |
1
b16989c1e3a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 457ccc12f14e041fe6dd7ca2a7e46a0237df4a21
iuc
parents:
0
diff
changeset
|
86 #if str($skip_rows) != '' |
b16989c1e3a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 457ccc12f14e041fe6dd7ca2a7e46a0237df4a21
iuc
parents:
0
diff
changeset
|
87 --skip_rows $skip_rows |
0
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
parents:
diff
changeset
|
88 #end if |
1
b16989c1e3a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 457ccc12f14e041fe6dd7ca2a7e46a0237df4a21
iuc
parents:
0
diff
changeset
|
89 #if str($sperc) != '' |
b16989c1e3a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 457ccc12f14e041fe6dd7ca2a7e46a0237df4a21
iuc
parents:
0
diff
changeset
|
90 --sperc $sperc |
0
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
parents:
diff
changeset
|
91 #end if |
1
b16989c1e3a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 457ccc12f14e041fe6dd7ca2a7e46a0237df4a21
iuc
parents:
0
diff
changeset
|
92 #if str($fperc) != '' |
b16989c1e3a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 457ccc12f14e041fe6dd7ca2a7e46a0237df4a21
iuc
parents:
0
diff
changeset
|
93 --fperc $fperc |
0
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
parents:
diff
changeset
|
94 #end if |
1
b16989c1e3a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 457ccc12f14e041fe6dd7ca2a7e46a0237df4a21
iuc
parents:
0
diff
changeset
|
95 #if str($stop) != '' |
b16989c1e3a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 457ccc12f14e041fe6dd7ca2a7e46a0237df4a21
iuc
parents:
0
diff
changeset
|
96 --stop $stop |
b16989c1e3a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 457ccc12f14e041fe6dd7ca2a7e46a0237df4a21
iuc
parents:
0
diff
changeset
|
97 #end if |
b16989c1e3a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 457ccc12f14e041fe6dd7ca2a7e46a0237df4a21
iuc
parents:
0
diff
changeset
|
98 #if str($ftop) != '' |
b16989c1e3a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 457ccc12f14e041fe6dd7ca2a7e46a0237df4a21
iuc
parents:
0
diff
changeset
|
99 --ftop $ftop |
0
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
parents:
diff
changeset
|
100 #end if |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
parents:
diff
changeset
|
101 ]]> |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
parents:
diff
changeset
|
102 </command> |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
parents:
diff
changeset
|
103 <inputs> |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
parents:
diff
changeset
|
104 <param argument="--lefse_input" type="data" format="tabular,txt,tsv" label="Input file" help="Identical to LEfSe input file"/> |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
parents:
diff
changeset
|
105 <conditional name="input_lefse_output"> |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
parents:
diff
changeset
|
106 <param name="input_lefse_output_test" type="select" label="Use a LEfSe output file as input?" help=""> |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
parents:
diff
changeset
|
107 <option value="true">Yes</option> |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
parents:
diff
changeset
|
108 <option value="false" selected="true">No</option> |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
parents:
diff
changeset
|
109 </param> |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
parents:
diff
changeset
|
110 <when value="true"> |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
parents:
diff
changeset
|
111 <param argument="--lefse_output" type="data" format="tabular" label="Input file corresponding to LEfSe output file"/> |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
parents:
diff
changeset
|
112 </when> |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
parents:
diff
changeset
|
113 <when value="false"/> |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
parents:
diff
changeset
|
114 </conditional> |
1
b16989c1e3a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 457ccc12f14e041fe6dd7ca2a7e46a0237df4a21
iuc
parents:
0
diff
changeset
|
115 <param argument="--annotations" type="text" optional="True" label="List which levels should be annotated in the tree" help="The levels must be in comma-separated form"/> |
b16989c1e3a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 457ccc12f14e041fe6dd7ca2a7e46a0237df4a21
iuc
parents:
0
diff
changeset
|
116 <param argument="--external_annotations" type="text" optional="True" label="List which levels should use the external legend for the annotation" help="The levels must be in comma-separated form"/> |
b16989c1e3a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 457ccc12f14e041fe6dd7ca2a7e46a0237df4a21
iuc
parents:
0
diff
changeset
|
117 <param argument="--background_levels" type="text" optional="True" label="List which levels should be highlight with a shaded background" help="The levels must be in comma-separated form"/> |
b16989c1e3a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 457ccc12f14e041fe6dd7ca2a7e46a0237df4a21
iuc
parents:
0
diff
changeset
|
118 <param argument="--background_clades" type="text" optional="True" label="List of the clades that should be highlight with a shaded background" help="The clades must be in comma-separated form"/> |
b16989c1e3a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 457ccc12f14e041fe6dd7ca2a7e46a0237df4a21
iuc
parents:
0
diff
changeset
|
119 <param argument="--background_colors" type="text" optional="True" label="List of color to use for the shaded background" help="Colors can be either in RGB or HSV (using a semi-colon to separate values, surrounded with ()). The different colors must be in comma-separated form"/> |
b16989c1e3a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 457ccc12f14e041fe6dd7ca2a7e46a0237df4a21
iuc
parents:
0
diff
changeset
|
120 <param argument="--title" type="text" optional="True" label="Title of the GraPhlAn plot" /> |
b16989c1e3a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 457ccc12f14e041fe6dd7ca2a7e46a0237df4a21
iuc
parents:
0
diff
changeset
|
121 <param argument="--title_font_size" type="integer" optional="True" label="Title font size"/> |
b16989c1e3a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 457ccc12f14e041fe6dd7ca2a7e46a0237df4a21
iuc
parents:
0
diff
changeset
|
122 <param argument="--def_clade_size" type="integer" optional="True" label="Default size for clades that are not found as biomarkers"/> |
b16989c1e3a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 457ccc12f14e041fe6dd7ca2a7e46a0237df4a21
iuc
parents:
0
diff
changeset
|
123 <param argument="--min_clade_size" type="integer" optional="True" label="Minimum value of clades that are biomarkers"/> |
b16989c1e3a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 457ccc12f14e041fe6dd7ca2a7e46a0237df4a21
iuc
parents:
0
diff
changeset
|
124 <param argument="--max_clade_size" type="integer" optional="True" label="Maximum value of clades that are biomarkers"/> |
b16989c1e3a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 457ccc12f14e041fe6dd7ca2a7e46a0237df4a21
iuc
parents:
0
diff
changeset
|
125 <param argument="--def_font_size" type="integer" optional="True" label="Default font size"/> |
b16989c1e3a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 457ccc12f14e041fe6dd7ca2a7e46a0237df4a21
iuc
parents:
0
diff
changeset
|
126 <param argument="--min_font_size" type="integer" optional="True" label="Minimum font size"/> |
b16989c1e3a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 457ccc12f14e041fe6dd7ca2a7e46a0237df4a21
iuc
parents:
0
diff
changeset
|
127 <param argument="--max_font_size" type="integer" optional="True" label="Maximum font size"/> |
b16989c1e3a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 457ccc12f14e041fe6dd7ca2a7e46a0237df4a21
iuc
parents:
0
diff
changeset
|
128 <param argument="--annotation_legend_font_size" type="integer" optional="True" label="Font size for the annotation legend"/> |
b16989c1e3a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 457ccc12f14e041fe6dd7ca2a7e46a0237df4a21
iuc
parents:
0
diff
changeset
|
129 <param argument="--abundance_threshold" type="float" optional="True" label="Minimun abundance value for a clade to be annotated"/> |
b16989c1e3a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 457ccc12f14e041fe6dd7ca2a7e46a0237df4a21
iuc
parents:
0
diff
changeset
|
130 <param argument="--most_abundant" type="integer" optional="True" label="Number of clades to highlight"/> |
b16989c1e3a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 457ccc12f14e041fe6dd7ca2a7e46a0237df4a21
iuc
parents:
0
diff
changeset
|
131 <param argument="--least_biomarkers" type="integer" optional="True" label="Minimum number of biomarkers to extract" help=" The taxonomy is parsed, and the level is choosen in order to have at least the specified number of biomarkers"/> |
b16989c1e3a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 457ccc12f14e041fe6dd7ca2a7e46a0237df4a21
iuc
parents:
0
diff
changeset
|
132 <param argument="--fname_row" type="integer" optional="True" label="Row number containing the names of the features" help="-1 specifies that no names are present in the matrix"/> |
b16989c1e3a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 457ccc12f14e041fe6dd7ca2a7e46a0237df4a21
iuc
parents:
0
diff
changeset
|
133 <param argument="--sname_row" type="integer" optional="True" label="Row number containing the names of the samples" help="-1 specifies that no names are present in the matrix"/> |
b16989c1e3a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 457ccc12f14e041fe6dd7ca2a7e46a0237df4a21
iuc
parents:
0
diff
changeset
|
134 <param argument="--metadata_rows" type="integer" optional="True" label="Row number to use as metadata"/> |
b16989c1e3a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 457ccc12f14e041fe6dd7ca2a7e46a0237df4a21
iuc
parents:
0
diff
changeset
|
135 <param argument="--skip_rows" type="text" optional="True" label="Row number to skip from the input file" help="The row numbers are indexed to 0 and comma separated"/> |
b16989c1e3a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 457ccc12f14e041fe6dd7ca2a7e46a0237df4a21
iuc
parents:
0
diff
changeset
|
136 <param argument="--sperc" type="float" optional="True" label="Percentile of sample value distribution for sample selection"/> |
b16989c1e3a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 457ccc12f14e041fe6dd7ca2a7e46a0237df4a21
iuc
parents:
0
diff
changeset
|
137 <param argument="--fperc" type="float" optional="True" label="Percentile of feature value distribution for sample selection"/> |
b16989c1e3a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 457ccc12f14e041fe6dd7ca2a7e46a0237df4a21
iuc
parents:
0
diff
changeset
|
138 <param argument="--stop" type="integer" optional="True" label="Number of top samples to select" help="The order is based on percentile specified by --sperc"/> |
b16989c1e3a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 457ccc12f14e041fe6dd7ca2a7e46a0237df4a21
iuc
parents:
0
diff
changeset
|
139 <param argument="--ftop" type="integer" optional="True" label="Number of top features to select" help="The order is based on percentile specified by --fperc"/> |
0
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
parents:
diff
changeset
|
140 </inputs> |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
parents:
diff
changeset
|
141 <outputs> |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
parents:
diff
changeset
|
142 <data format="txt" name="tree" label="${tool.name} on ${on_string}: Tree" /> |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
parents:
diff
changeset
|
143 <data format="txt" name="annotation" label="${tool.name} on ${on_string}: Annotation" /> |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
parents:
diff
changeset
|
144 </outputs> |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
parents:
diff
changeset
|
145 <tests> |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
parents:
diff
changeset
|
146 <test> |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
parents:
diff
changeset
|
147 <param name="lefse_input" value="input_profile.tabular"/> |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
parents:
diff
changeset
|
148 <param name="input_lefse_output_test" value="no" /> |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
parents:
diff
changeset
|
149 <param name="annotations" value=""/> |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
parents:
diff
changeset
|
150 <param name="external_annotations" value=""/> |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
parents:
diff
changeset
|
151 <param name="background_levels" value=""/> |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
parents:
diff
changeset
|
152 <param name="background_clades" value=""/> |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
parents:
diff
changeset
|
153 <param name="background_colors" value=""/> |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
parents:
diff
changeset
|
154 <param name="title" value=""/> |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
parents:
diff
changeset
|
155 <param name="title_font_size" value="15"/> |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
parents:
diff
changeset
|
156 <param name="def_clade_size" value="10"/> |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
parents:
diff
changeset
|
157 <param name="min_clade_size" value="20"/> |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
parents:
diff
changeset
|
158 <param name="max_clade_size" value="200"/> |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
parents:
diff
changeset
|
159 <param name="def_font_size" value="10"/> |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
parents:
diff
changeset
|
160 <param name="min_font_size" value="8"/> |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
parents:
diff
changeset
|
161 <param name="max_font_size" value="12"/> |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
parents:
diff
changeset
|
162 <param name="annotation_legend_font_size" value="10"/> |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
parents:
diff
changeset
|
163 <param name="abundance_threshold" value="20.0"/> |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
parents:
diff
changeset
|
164 <param name="fname_row" value="0"/> |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
parents:
diff
changeset
|
165 <param name="sname_row" value="0" /> |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
parents:
diff
changeset
|
166 <output name="annotation" file="annotation_output.txt"/> |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
parents:
diff
changeset
|
167 <output name="tree" file="tree_output.txt"/> |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
parents:
diff
changeset
|
168 </test> |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
parents:
diff
changeset
|
169 </tests> |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
parents:
diff
changeset
|
170 <help><![CDATA[ |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
parents:
diff
changeset
|
171 |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
parents:
diff
changeset
|
172 **What it does** |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
parents:
diff
changeset
|
173 |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
parents:
diff
changeset
|
174 export2graphlan is a conversion software tool to produce both annotation and tree file for GraPhlAn. It can convert MetaPhlAn, LEfSe, and/or HUMAnN output to GraPhlAn input format |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
parents:
diff
changeset
|
175 |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
parents:
diff
changeset
|
176 In particular, the annotation file tries to highlight specific sub-trees deriving automatically from input file what nodes are important. |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
parents:
diff
changeset
|
177 |
2
635c90a27692
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 1a2cbe050c6b172147064cb53b16d6833f138b68
iuc
parents:
1
diff
changeset
|
178 For more information, check the `user manual <https://github.com/SegataLab/export2graphlan/>`_. |
0
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
parents:
diff
changeset
|
179 |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
parents:
diff
changeset
|
180 ]]></help> |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
parents:
diff
changeset
|
181 <citations> |
2
635c90a27692
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 1a2cbe050c6b172147064cb53b16d6833f138b68
iuc
parents:
1
diff
changeset
|
182 <citation type="doi">10.7717/peerj.1029</citation> |
0
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
parents:
diff
changeset
|
183 </citations> |
ed1becc01910
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ commit 2411a616fc3865b53a03d40bce5b434d0ce44134
iuc
parents:
diff
changeset
|
184 </tool> |