Mercurial > repos > jjohnson > eggnog_mapper

annotate test-data/make_comp_file.sh @ 2:a74d61dbd155 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit f431329cd1c7f8a6014207a4ebfd9ffaa67e5497-dirty
author jjohnson
date Mon, 04 Nov 2019 16:38:44 -0500
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a74d61dbd155 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit f431329cd1c7f8a6014207a4ebfd9ffaa67e5497-dirty
jjohnson
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1 #!/bin/bash
a74d61dbd155 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit f431329cd1c7f8a6014207a4ebfd9ffaa67e5497-dirty
jjohnson
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2
a74d61dbd155 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit f431329cd1c7f8a6014207a4ebfd9ffaa67e5497-dirty
jjohnson
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3 base_path=$1
a74d61dbd155 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit f431329cd1c7f8a6014207a4ebfd9ffaa67e5497-dirty
jjohnson
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4
a74d61dbd155 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit f431329cd1c7f8a6014207a4ebfd9ffaa67e5497-dirty
jjohnson
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5 emapper.py \
a74d61dbd155 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit f431329cd1c7f8a6014207a4ebfd9ffaa67e5497-dirty
jjohnson
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6 -i $base_path/test-data/nlim_fragment.fasta \
a74d61dbd155 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit f431329cd1c7f8a6014207a4ebfd9ffaa67e5497-dirty
jjohnson
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7 --output HMM_nlim \
a74d61dbd155 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit f431329cd1c7f8a6014207a4ebfd9ffaa67e5497-dirty
jjohnson
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8 --output_dir $base_path/test-data \
a74d61dbd155 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit f431329cd1c7f8a6014207a4ebfd9ffaa67e5497-dirty
jjohnson
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9 --override \
a74d61dbd155 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit f431329cd1c7f8a6014207a4ebfd9ffaa67e5497-dirty
jjohnson
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10 --database $base_path/test-data/cached_locally/hmmdb_levels/ENOG411CB2I/ENOG411CB2I \
a74d61dbd155 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit f431329cd1c7f8a6014207a4ebfd9ffaa67e5497-dirty
jjohnson
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11 --data_dir $base_path/test-data/cached_locally \
a74d61dbd155 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit f431329cd1c7f8a6014207a4ebfd9ffaa67e5497-dirty
jjohnson
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12 --no_refine\
a74d61dbd155 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit f431329cd1c7f8a6014207a4ebfd9ffaa67e5497-dirty
jjohnson
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13 --no_annot \
a74d61dbd155 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit f431329cd1c7f8a6014207a4ebfd9ffaa67e5497-dirty
jjohnson
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14 --no_file_comments
a74d61dbd155 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit f431329cd1c7f8a6014207a4ebfd9ffaa67e5497-dirty
jjohnson
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15
a74d61dbd155 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit f431329cd1c7f8a6014207a4ebfd9ffaa67e5497-dirty
jjohnson
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16 emapper.py \
a74d61dbd155 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit f431329cd1c7f8a6014207a4ebfd9ffaa67e5497-dirty
jjohnson
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17 -i $base_path/test-data/nlim_fragment.fasta \
a74d61dbd155 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit f431329cd1c7f8a6014207a4ebfd9ffaa67e5497-dirty
jjohnson
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18 --output DIA_nlim \
a74d61dbd155 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit f431329cd1c7f8a6014207a4ebfd9ffaa67e5497-dirty
jjohnson
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19 --output_dir $base_path/test-data \
a74d61dbd155 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit f431329cd1c7f8a6014207a4ebfd9ffaa67e5497-dirty
jjohnson
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20 --override \
a74d61dbd155 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit f431329cd1c7f8a6014207a4ebfd9ffaa67e5497-dirty
jjohnson
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21 -m diamond \
a74d61dbd155 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit f431329cd1c7f8a6014207a4ebfd9ffaa67e5497-dirty
jjohnson
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22 --data_dir $base_path/test-data/cached_locally \
a74d61dbd155 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit f431329cd1c7f8a6014207a4ebfd9ffaa67e5497-dirty
jjohnson
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23 --no_file_comments \
a74d61dbd155 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit f431329cd1c7f8a6014207a4ebfd9ffaa67e5497-dirty
jjohnson
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24 --no_annot