Mercurial > repos > galaxyp > eggnog_mapper

annotate test-data/make_comp_file.sh @ 6:3cb37af59360 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
author galaxyp
date Sat, 05 Sep 2020 07:21:28 +0000
parents f4e5279b5d10
children
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f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
1 #!/bin/bash
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
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2
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
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3 base_path=$1
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
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4
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
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5 emapper.py \
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
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6 -i $base_path/test-data/nlim_fragment.fasta \
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
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7 --output DIA_nlim \
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
diff changeset
8 --output_dir $base_path/test-data \
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
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9 --override \
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
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10 -m diamond \
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
parents:
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11 --data_dir $base_path/test-data/cached_locally \
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
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12 --no_file_comments \
f4e5279b5d10 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 9dbc338105e83091a636166030f618ec881c5f6f
galaxyp
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13 --no_annot