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annotate umiout.sh @ 13:18d6b8c65512 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 1971e35a365a91ae36c990b374a552a46196e888
author bgruening
date Wed, 29 Oct 2025 10:45:57 +0000
parents b579f36923d9
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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b579f36923d9 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit c17bc974bf9bbaa1fc1e47ea72162fd244f0e612"
bgruening
parents:
diff changeset
1 #!/usr/bin/bash
b579f36923d9 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit c17bc974bf9bbaa1fc1e47ea72162fd244f0e612"
bgruening
parents:
diff changeset
2
13
18d6b8c65512 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 1971e35a365a91ae36c990b374a552a46196e888
bgruening
parents: 2
diff changeset
3 set -e
18d6b8c65512 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 1971e35a365a91ae36c990b374a552a46196e888
bgruening
parents: 2
diff changeset
4
18d6b8c65512 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 1971e35a365a91ae36c990b374a552a46196e888
bgruening
parents: 2
diff changeset
5 mkdir -p fixed;
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b579f36923d9 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit c17bc974bf9bbaa1fc1e47ea72162fd244f0e612"
bgruening
parents:
diff changeset
6 for file in ./umiout/*;
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18d6b8c65512 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 1971e35a365a91ae36c990b374a552a46196e888
bgruening
parents: 2
diff changeset
7 do
18d6b8c65512 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 1971e35a365a91ae36c990b374a552a46196e888
bgruening
parents: 2
diff changeset
8 prefix="${file%.dot.gz}";
18d6b8c65512 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 1971e35a365a91ae36c990b374a552a46196e888
bgruening
parents: 2
diff changeset
9 prefix="${prefix/.\/umiout\//}";
18d6b8c65512 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 1971e35a365a91ae36c990b374a552a46196e888
bgruening
parents: 2
diff changeset
10 gunzip "$file";
18d6b8c65512 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 1971e35a365a91ae36c990b374a552a46196e888
bgruening
parents: 2
diff changeset
11 sed "s/umiout\/$prefix.dot.gz/$prefix/" "umiout/$prefix.dot" > "fixed/$prefix.dot";
18d6b8c65512 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 1971e35a365a91ae36c990b374a552a46196e888
bgruening
parents: 2
diff changeset
12 dot -Tpdf "fixed/$prefix.dot" -o "fixed/$prefix.pdf";
2
b579f36923d9 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit c17bc974bf9bbaa1fc1e47ea72162fd244f0e612"
bgruening
parents:
diff changeset
13 done
b579f36923d9 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit c17bc974bf9bbaa1fc1e47ea72162fd244f0e612"
bgruening
parents:
diff changeset
14 ls fixed