Mercurial > repos > rnateam > graphclust_align_cluster

annotate call_rscape.sh @ 1:953353eacec2 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tools/GraphClust/AlignCluster commit 5fe196bd60c65c884ae1685d4b7fb33119564fa7
author rnateam
date Sun, 28 Oct 2018 18:52:14 -0400
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953353eacec2 planemo upload for repository https://github.com/bgruening/galaxytools/tools/GraphClust/AlignCluster commit 5fe196bd60c65c884ae1685d4b7fb33119564fa7
rnateam
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1 #!/bin/bash
953353eacec2 planemo upload for repository https://github.com/bgruening/galaxytools/tools/GraphClust/AlignCluster commit 5fe196bd60c65c884ae1685d4b7fb33119564fa7
rnateam
parents:
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953353eacec2 planemo upload for repository https://github.com/bgruening/galaxytools/tools/GraphClust/AlignCluster commit 5fe196bd60c65c884ae1685d4b7fb33119564fa7
rnateam
parents:
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3 num_bps=$(grep "SS_cons" $2 | awk '{print $3}' | tr -d '.' | tr -d '\n' | wc -c)
953353eacec2 planemo upload for repository https://github.com/bgruening/galaxytools/tools/GraphClust/AlignCluster commit 5fe196bd60c65c884ae1685d4b7fb33119564fa7
rnateam
parents:
diff changeset
4 if [ $num_bps -gt 2 ]; then
953353eacec2 planemo upload for repository https://github.com/bgruening/galaxytools/tools/GraphClust/AlignCluster commit 5fe196bd60c65c884ae1685d4b7fb33119564fa7
rnateam
parents:
diff changeset
5 R-scape --outdir $1 $2
953353eacec2 planemo upload for repository https://github.com/bgruening/galaxytools/tools/GraphClust/AlignCluster commit 5fe196bd60c65c884ae1685d4b7fb33119564fa7
rnateam
parents:
diff changeset
6 else
953353eacec2 planemo upload for repository https://github.com/bgruening/galaxytools/tools/GraphClust/AlignCluster commit 5fe196bd60c65c884ae1685d4b7fb33119564fa7
rnateam
parents:
diff changeset
7 echo "No consensus structure, R-scape skipped";
953353eacec2 planemo upload for repository https://github.com/bgruening/galaxytools/tools/GraphClust/AlignCluster commit 5fe196bd60c65c884ae1685d4b7fb33119564fa7
rnateam
parents:
diff changeset
8 fi