Mercurial > repos > brinkmanlab > mauve_contig_mover

annotate mcm_final.sh @ 6:4931255f2fcc draft

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"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 25b7aeca541e258a2bff5d0e34e9298996b4a47b"
author brinkmanlab
date Fri, 20 Nov 2020 18:58:52 +0000
parents c14690ec0c9f
children
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c14690ec0c9f "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
diff changeset
1 #!/usr/bin/env bash
c14690ec0c9f "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
diff changeset
2 ln -sf output/`ls -1 output | tail -n1` final
c14690ec0c9f "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
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3 mv "`ls -1 final/*.backbone | tail -n1`" final.backbone
c14690ec0c9f "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
diff changeset
4 mv "`ls -1 final/*_contigs.tab | tail -n1`" final.contigs.tab
c14690ec0c9f "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
diff changeset
5 mv "`ls -1 final/*.fas | tail -n1`" final.reordered
c14690ec0c9f "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
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6
c14690ec0c9f "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
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7 FEATURES="`ls -1 final/*_features.tab 2>/dev/null | tail -n1`"
c14690ec0c9f "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
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8 if [[ -w ${FEATURES} ]]; then
c14690ec0c9f "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
diff changeset
9 mv "${FEATURES}" final.features.tab
c14690ec0c9f "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
diff changeset
10 fi
c14690ec0c9f "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
parents:
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11