Updating functions

justincbagley · Dec 23, 2020 · e7d3f4d · e7d3f4d
1 parent c52a136
commit e7d3f4d
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Showing 9 changed files with 18 additions and 9 deletions.
diff --git a/bin/FASTAsummary b/bin/FASTAsummary
@@ -419,7 +419,8 @@ if [[ "$MY_DEBUG_MODE_SWITCH" != "0" ]]; then set +xv; fi
 
 
 ############ CREATE USAGE & HELP TEXTS
-USAGE="Usage: $(basename "$0") [OPTION]...
+USAGE="
+Usage: $(basename "$0") [OPTION]...
 
  ${bold}Options:${reset}
   -i   inputFASTA (def: NULL) input FASTA filename

diff --git a/bin/NEXUS2MultiPHYLIP b/bin/NEXUS2MultiPHYLIP
@@ -516,7 +516,8 @@ echo ""
 
 
 ############ CREATE USAGE & HELP TEXTS
-USAGE="Usage: $(basename "$0") [OPTION]...
+USAGE="
+Usage: $(basename "$0") [OPTION]...
 
  ${bold}Options:${reset}
   -i   inputNEXUS (def: NULL) mandatory input NEXUS file in sequential NEXUS format

diff --git a/bin/PHYLIP2Mega b/bin/PHYLIP2Mega
@@ -343,7 +343,8 @@ echo ""
 
 
 ############ CREATE USAGE & HELP TEXTS
-USAGE="Usage: $(basename "$0") [OPTION]...
+USAGE="
+Usage: $(basename "$0") [OPTION]...
 
  ${bold}Options:${reset}
   -i   inputPHYLIP (def: NULL) input PHYLIP filename; run on this individual PHYLIP file

diff --git a/bin/RogueNaRokRunner b/bin/RogueNaRokRunner
@@ -262,7 +262,8 @@ echo ""
 
 
 ############ CREATE USAGE & HELP TEXTS
-USAGE="Usage: $(basename "$0") [OPTION]...
+USAGE="
+Usage: $(basename "$0") [OPTION]...
 
  ${bold}Options:${reset}
   -i   inputFile (def: NULL) input DNA sequence alignment filename

diff --git a/bin/batchRunFolders b/bin/batchRunFolders
@@ -535,7 +535,8 @@ if [[ "$MY_DEBUG_MODE_SWITCH" != "0" ]]; then set +xv; fi
 # MY_DEBUG_MODE_SWITCH=0
 
 ############ CREATE USAGE & HELP TEXTS
-USAGE="Usage: $(basename "$0") [OPTION]...
+USAGE="
+Usage: $(basename "$0") [OPTION]...
 
  ${bold}Options:${reset}
   -i, --input     inputList (def: NULL) name of file containing list of input files

diff --git a/bin/calcAlignmentPIS b/bin/calcAlignmentPIS
@@ -419,7 +419,8 @@ MY_PIS_THRESHOLD_SWITCH=0
 KEEP_R_FILES_SWITCH=1
 
 ############ CREATE USAGE & HELP TEXTS
-USAGE="Usage: $(basename "$0") [OPTION]...
+USAGE="
+Usage: $(basename "$0") [OPTION]...
 
  ${bold}Options:${reset}
   -i   inputFASTA (def: NULL) input FASTA filename

diff --git a/bin/dropRandomHap b/bin/dropRandomHap
@@ -630,7 +630,8 @@ if [[ "$MY_DEBUG_MODE_SWITCH" != "0" ]]; then set +xv; fi
 # MY_DEBUG_MODE_SWITCH=0
 
 ############ CREATE USAGE & HELP TEXTS
-USAGE="Usage: $(basename "$0") [OPTION]...
+USAGE="
+Usage: $(basename "$0") [OPTION]...
 
  ${bold}Options:${reset}
   -i, --input     inputPHYLIP (def: NULL) name of input PHYLIP DNA sequence alignment file

diff --git a/bin/dropTaxa b/bin/dropTaxa
@@ -526,7 +526,8 @@ if [[ "$MY_DEBUG_MODE_SWITCH" != "0" ]]; then set +xv; fi
 
 
 ############ CREATE USAGE & HELP TEXTS
-USAGE="Usage: $(basename "$0") [OPTION]...
+USAGE="
+Usage: $(basename "$0") [OPTION]...
 
  ${bold}Options:${reset}
   -i   inputFile (def: NULL) name of input DNA sequence alignment file

diff --git a/bin/splitPHYLIP b/bin/splitPHYLIP
@@ -341,7 +341,8 @@ echo ""
 # MY_VERBOSE_OUT_SWITCH=0
 
 ############ CREATE USAGE & HELP TEXTS
-USAGE="Usage: $(basename "$0") [OPTION]...
+USAGE="
+Usage: $(basename "$0") [OPTION]...
 
  ${bold}Options:${reset}
   -i, --input     inputPHYLIP (def: NULL) input PHYLIP-formatted DNA sequence alignment file