Mercurial > repos > florianbegusch > qiime2_suite
comparison qiime2/qiime_diversity_beta-correlation.xml @ 4:914fa4daf16a draft
Fixes
author | florianbegusch |
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date | Wed, 31 Jul 2019 03:06:00 -0400 |
parents | 370e0b6e9826 |
children | de4c22a52df4 |
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3:558645416841 | 4:914fa4daf16a |
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6 </requirements> | 6 </requirements> |
7 <command><![CDATA[ | 7 <command><![CDATA[ |
8 qiime diversity beta-correlation | 8 qiime diversity beta-correlation |
9 | 9 |
10 --i-distance-matrix=$idistancematrix | 10 --i-distance-matrix=$idistancematrix |
11 | |
12 | |
13 | |
14 #if '__sq__' in str($mmetadatacolumn): | |
15 #set $mmetadatacolumn_temp = $mmetadatacolumn.replace('__sq__', "'") | |
16 #set $mmetadatacolumn = $mmetadatacolumn_temp | |
17 #end if | |
18 | |
11 --m-metadata-column="$mmetadatacolumn" | 19 --m-metadata-column="$mmetadatacolumn" |
20 | |
21 | |
12 | 22 |
13 #if str($pmethod) != 'None': | 23 #if str($pmethod) != 'None': |
14 --p-method=$pmethod | 24 --p-method=$pmethod |
15 #end if | 25 #end if |
16 | 26 |
20 | 30 |
21 #if $pintersectids: | 31 #if $pintersectids: |
22 --p-intersect-ids | 32 --p-intersect-ids |
23 #end if | 33 #end if |
24 | 34 |
35 | |
36 | |
37 | |
38 #if '__sq__' in str($plabel1): | |
39 #set $plabel1_temp = $plabel1.replace('__sq__', "'") | |
40 #set $plabel1 = $plabel1_temp | |
41 #end if | |
42 | |
25 #if str($plabel1): | 43 #if str($plabel1): |
26 --p-label1="$plabel1" | 44 --p-label1="$plabel1" |
45 #end if | |
46 | |
47 | |
48 | |
49 #if '__sq__' in str($plabel2): | |
50 #set $plabel2_temp = $plabel2.replace('__sq__', "'") | |
51 #set $plabel2 = $plabel2_temp | |
27 #end if | 52 #end if |
28 | 53 |
29 #if str($plabel2): | 54 #if str($plabel2): |
30 --p-label2="$plabel2" | 55 --p-label2="$plabel2" |
31 #end if | 56 #end if |
57 | |
58 | |
32 | 59 |
33 #if $input_files_mmetadatafile: | 60 #if $input_files_mmetadatafile: |
34 #def list_dict_to_string(list_dict): | 61 #def list_dict_to_string(list_dict): |
35 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name') | 62 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name') |
36 #for d in list_dict[1:]: | 63 #for d in list_dict[1:]: |
57 <option value="spearman">spearman</option> | 84 <option value="spearman">spearman</option> |
58 <option value="pearson">pearson</option> | 85 <option value="pearson">pearson</option> |
59 </param> | 86 </param> |
60 <param label="--p-permutations: INTEGER Range(0, None) The number of permutations to be run when computing p-values. Supplying a value of zero will disable permutation testing and p-values will not be calculated (this results in *much* quicker execution time if p-values are not desired). [default: 999]" name="ppermutations" optional="True" type="integer" min="0" value="999"/> | 87 <param label="--p-permutations: INTEGER Range(0, None) The number of permutations to be run when computing p-values. Supplying a value of zero will disable permutation testing and p-values will not be calculated (this results in *much* quicker execution time if p-values are not desired). [default: 999]" name="ppermutations" optional="True" type="integer" min="0" value="999"/> |
61 <param label="--p-intersect-ids: --p-no-intersect-ids If supplied, IDs that are not found in both distance matrices will be discarded before applying the Mantel test. Default behavior is to error on any mismatched IDs. [default: False]" name="pintersectids" selected="False" type="boolean"/> | 88 <param label="--p-intersect-ids: --p-no-intersect-ids If supplied, IDs that are not found in both distance matrices will be discarded before applying the Mantel test. Default behavior is to error on any mismatched IDs. [default: False]" name="pintersectids" selected="False" type="boolean"/> |
62 <param label="--p-label1: TEXT Label for `distance-matrix` in the output visualization. [default: 'Metadata']" name="plabel1" optional="True" type="text" value="'Metadata'"/> | 89 <param label="--p-label1: TEXT Label for `distance-matrix` in the output visualization. [default: 'Metadata']" name="plabel1" optional="True" type="text" value="Metadata"/> |
63 <param label="--p-label2: TEXT Label for `metadata-distance-matrix` in the output visualization. [default: 'Distance Matrix']" name="plabel2" optional="True" type="text" value="'Distance Matrix'"/> | 90 <param label="--p-label2: TEXT Label for `metadata-distance-matrix` in the output visualization. [default: 'Distance Matrix']" name="plabel2" optional="True" type="text" value="Distance Matrix"/> |
64 <repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file"> | 91 <repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file [required]"> |
65 <param label="--m-metadata-file" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" /> | 92 <param label="--m-metadata-file" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" /> |
66 </repeat> | 93 </repeat> |
67 </inputs> | 94 </inputs> |
68 <outputs> | 95 <outputs> |
69 <data format="qza" label="${tool.name} on ${on_string}: metadatadistancematrix.qza" name="ometadatadistancematrix"/> | 96 <data format="qza" label="${tool.name} on ${on_string}: metadatadistancematrix.qza" name="ometadatadistancematrix"/> |