Mercurial > repos > malex > gait_gm
annotate macros.xml @ 2:2c218a253d56 draft default tip
"planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b"
| author | malex |
|---|---|
| date | Thu, 29 Jul 2021 20:48:10 +0000 |
| parents | ec9ee8edb84d |
| children |
| rev | line source |
|---|---|
| 1 | 1 <?xml version="1.0" ?> |
| 2 <macros> | |
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2c218a253d56
"planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b"
malex
parents:
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3 <token name="@WRAPPER_VERSION@">21.7.22</token> |
| 1 | 4 <xml name="requirements"> |
| 5 <requirements> | |
| 6 <requirement type="package" version="@WRAPPER_VERSION@">gait-gm</requirement> | |
| 7 <yield/> | |
| 8 </requirements> | |
| 9 </xml> <xml name="citations"> | |
| 10 <citations> | |
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2c218a253d56
"planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b"
malex
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11 <citation type="bibtex">@ARTICLE{Mor21,gaitgm |
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2c218a253d56
"planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b"
malex
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12 author = {Danille E Mor, Francisco Huertas, Alison M Morse, Rachel Kaletsky, Coleen T Murphy, Vrinda Kalia, Gary W Miller, Oleksandr Moskalenko, Ana conesa, Lauren M McIntyre}, |
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2c218a253d56
"planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b"
malex
parents:
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13 title = {GAIT-GM integrative cross-omics analyses reveal cholinergic defects in a C. elegans model of Parkinson's disease}, |
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2c218a253d56
"planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b"
malex
parents:
1
diff
changeset
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14 journal = {BMC Genomics}, |
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2c218a253d56
"planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b"
malex
parents:
1
diff
changeset
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15 year = {submitted} |
| 1 | 16 }</citation> |
| 17 </citations> | |
| 18 </xml> | |
| 19 | |
| 20 <token name="@TIP_AND_WARNING@"> | |
| 21 **TIP:** If your data is not TAB delimited, use *Text Manipulation->Convert* | |
| 22 | |
| 23 **WARNINGS:** | |
| 24 | |
| 25 (1) SampleIDs in the wide data that have no matching name in the design file, as well as sampleIDs in the design file that have no match in data will be included in the analysis. | |
| 26 (2) This script automatically removes spaces and special characters from strings. | |
| 27 (3) If a compound/feature name starts with a number it will prepend an '_'. | |
| 28 (4) Input names are case sensitive and must match exactly (e.g use 'Feature' not 'feature'). | |
| 29 </token> | |
| 30 <token name="@WIDE@"> | |
| 31 **Wide Formatted Dataset** | |
| 32 | |
| 33 A wide formatted dataset that contains measurements for each sample: | |
| 34 | |
| 35 +---------+---------+---------+---------+-----+ | |
| 36 | Feature | sample1 | sample2 | sample3 | ... | | |
| 37 +=========+=========+=========+=========+=====+ | |
| 38 | one | 10 | 20 | 10 | ... | | |
| 39 +---------+---------+---------+---------+-----+ | |
| 40 | two | 5 | 22 | 30 | ... | | |
| 41 +---------+---------+---------+---------+-----+ | |
| 42 | three | 30 | 27 | 2 | ... | | |
| 43 +---------+---------+---------+---------+-----+ | |
| 44 | four | 32 | 17 | 8 | ... | | |
| 45 +---------+---------+---------+---------+-----+ | |
| 46 | ... | ... | ... | ... | ... | | |
| 47 +---------+---------+---------+---------+-----+ | |
| 48 | |
| 49 **NOTE:** The 'Feature' column defines the rows within a wide formatted dataset. | |
| 50 </token> | |
| 51 <token name="@METADATA@"> | |
| 52 **Design File** | |
| 53 | |
| 54 A Design file relating samples to various groups/treatment: | |
| 55 | |
| 56 +----------+--------+ | |
| 57 | sampleID | group | | |
| 58 +==========+========+ | |
| 59 | sample1 | g1 | | |
| 60 +----------+--------+ | |
| 61 | sample2 | g1 | | |
| 62 +----------+--------+ | |
| 63 | sample3 | g1 | | |
| 64 +----------+--------+ | |
| 65 | sample4 | g2 | | |
| 66 +----------+--------+ | |
| 67 | sample5 | g2 | | |
| 68 +----------+--------+ | |
| 69 | sample6 | g2 | | |
| 70 +----------+--------+ | |
| 71 | ... | ... | | |
| 72 +----------+--------+ | |
| 73 | |
| 74 **NOTE:** You must have a column named **sampleID** and the values in this column must match the column names in the wide dataset. | |
| 75 </token> | |
| 76 <token name="@FLAGS@"> | |
| 77 **Flag File:** | |
| 78 | |
| 79 A wide formated dataset that contains flags for each sample or feature: | |
| 80 | |
| 81 +----------+---------+---------+---------+-----+ | |
| 82 | Feature | flag_A | flag_B | flag_C | ... | | |
| 83 +==========+=========+=========+=========+=====+ | |
| 84 | one | 0 | 0 | 0 | ... | | |
| 85 +----------+---------+---------+---------+-----+ | |
| 86 | two | 0 | 1 | 1 | ... | | |
| 87 +----------+---------+---------+---------+-----+ | |
| 88 | three | 0 | 1 | 0 | ... | | |
| 89 +----------+---------+---------+---------+-----+ | |
| 90 | four | 1 | 0 | 0 | ... | | |
| 91 +----------+---------+---------+---------+-----+ | |
| 92 | ... | ... | ... | ... | ... | | |
| 93 +----------+---------+---------+---------+-----+ | |
| 94 | |
| 95 </token> | |
| 96 <token name="@MZRTFILE@"> | |
| 97 **M/Z RT File:** | |
| 98 | |
| 99 A wide formated dataset that contains M/Z and RT measurements for each sample: | |
| 100 | |
| 101 +----------+--------+----------------+ | |
| 102 | sampleID | M/Z | Retention Time | | |
| 103 +==========+========+================+ | |
| 104 | sample1 | 0.1556 | 0.253618769 | | |
| 105 +----------+--------+----------------+ | |
| 106 | sample2 | 0.1675 | 0.327658519 | | |
| 107 +----------+--------+----------------+ | |
| 108 | sample3 | 0.1341 | 0.156587769 | | |
| 109 +----------+--------+----------------+ | |
| 110 | sample4 | 0.2341 | 0.153658165 | | |
| 111 +----------+--------+----------------+ | |
| 112 | sample5 | 0.4557 | 0.315765787 | | |
| 113 +----------+--------+----------------+ | |
| 114 | sample6 | 0.1879 | 0.253655765 | | |
| 115 +----------+--------+----------------+ | |
| 116 | ... | ... | ... | | |
| 117 +----------+--------+----------------+ | |
| 118 | |
| 119 </token> | |
| 120 <token name="@GROUP_OPTIONAL@"> | |
| 121 **Group/Treatment [Optional]** | |
| 122 | |
| 123 - Name of the column in your Design File that contains group classifications. | |
| 124 </token> | |
| 125 <token name="@GROUP@"> | |
| 126 **Group/Treatment** | |
| 127 | |
| 128 - Name of the column in your Design File that contains group classifications. | |
| 129 </token> | |
| 130 <token name="@UNIQID@"> | |
| 131 **Unique Feature ID** | |
| 132 | |
| 133 - Name of the column in your Wide Dataset that has unique Feature IDs. | |
| 134 </token> | |
| 135 <token name="@RUNORDER@"> | |
| 136 **Run Order ID** | |
| 137 | |
| 138 - The column name in your Design file that contains the order samples were run. | |
| 139 </token> | |
| 140 <token name="@RUNORDER_OPTIONAL@"> | |
| 141 **Run Order ID [Optional]** | |
| 142 | |
| 143 - The column name in your Design file that contains the order samples were run. | |
| 144 </token> | |
| 145 </macros> |