Merge pull request #1832 from milaboratory/mixcr-regression-tests/fixes

Regression tests changes in the fixes
milaboratory · Oct 23, 2024 · 0cbd8c2 · 0cbd8c2
2 parents 8953bae + acdb58a
commit 0cbd8c2
Showing 1 changed file with 3 additions and 3 deletions.
diff --git a/regression/cli-help/findShmTrees.txt b/regression/cli-help/findShmTrees.txt
@@ -1,6 +1,6 @@
 Usage: mixcr findShmTrees [--v-gene-names <gene_name>]... [--j-gene-names <gene_name>]...
                           [--cdr3-lengths <n>]... [--min-count <n>] [--productive-only]
-                          [--alleles-search-could-be-skipped] [--dont-combine-tree-by-cells] [-O
+                          [--dont-combine-tree-by-cells] [--alleles-search-could-be-skipped] [-O
                           <key=value>]... [--report <path>] [--json-report <path>]
                           [--use-local-temp] [--threads <n>] [--force-overwrite] [--no-warnings]
                           [--verbose] [--help] (input_file.clns|directory)... output_file.shmt
@@ -20,6 +20,8 @@ All inputs must be fully covered by the same feature, have the same library prod
       --min-count <n>        Filter clones with counts great or equal to that parameter
       --productive-only      Build trees only on productive clones (no stop codons in all features
                                and no out of frame in CDR3)
+      --dont-combine-tree-by-cells
+                             In case of data with cell groups, will not combine trees by cells.
       --alleles-search-could-be-skipped
                              In specific cases preliminary search for alleles could be skipped. For
                                example:
@@ -30,8 +32,6 @@ All inputs must be fully covered by the same feature, have the same library prod
                               - you have homogeneous specie and have a library with all presented
                                genes beforehand (but better to run `findAlleles` to check that
                                there is no diversity)
-      --dont-combine-tree-by-cells
-                             In case of data with cell groups, will not combine trees by cells.
   -O  <key=value>            Overrides default build SHM parameter values
   -r, --report <path>        Report file (human readable version, see `-j / --json-report` for
                                machine readable report).