# HG changeset patch
# User iuc
# Date 1772465798 0
# Node ID 9dce901753b9b25ccca3fd747ff0078174c973eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign commit bab03e73ec98fc53e8c0eb899ab8144a775d331a
diff -r 000000000000 -r 9dce901753b9 cialign.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/cialign.xml Mon Mar 02 15:36:38 2026 +0000
@@ -0,0 +1,1254 @@
+
+ clean, visualise and analyse a multiple sequence alignment
+
+ macros.xml
+
+
+ CIAlign --version
+ input.fasta &&
+ CIAlign --infile input.fasta
+ #else:
+ CIAlign --infile '$input'
+ #end if
+ --outfile_stem 'output'
+
+ ###### Basic Options
+ $basic_options.all
+ $basic_options.clean
+ $basic_options.visualise
+ $basic_options.interpret
+
+ ###### Cleaning Options
+ ### Remove Divergent options
+ #if str($cleaning_options.remove_divergent_cond.remove_divergent_param) == "true":
+ --remove_divergent
+ --remove_divergent_minperc $cleaning_options.remove_divergent_cond.remove_divergent_minperc
+ #for $s in $cleaning_options.remove_divergent_cond.remove_divergent_retain_seqs
+ --remove_divergent_retain '$s.remove_divergent_retain'
+ #end for
+ #for $s in $cleaning_options.remove_divergent_cond.remove_divergent_retain_strings
+ --remove_divergent_retain_str '$s.remove_divergent_retain_str'
+ #end for
+ #end if
+
+ ### Remove Insertions options
+ #if str($cleaning_options.remove_insertions_cond.remove_insertions_param) == "true":
+ --remove_insertions
+ --insertion_min_size $cleaning_options.remove_insertions_cond.insertion_min_size
+ --insertion_max_size $cleaning_options.remove_insertions_cond.insertion_max_size
+ --insertion_min_flank $cleaning_options.remove_insertions_cond.insertion_min_flank
+ --insertion_min_perc $cleaning_options.remove_insertions_cond.insertion_min_perc
+ #end if
+
+ ### Crop Ends options
+ #if str($cleaning_options.crop_ends_cond.crop_ends_param) == "true":
+ --crop_ends
+ --crop_ends_mingap_perc $cleaning_options.crop_ends_cond.crop_ends_mingap_perc
+ --crop_ends_redefine_perc $cleaning_options.crop_ends_cond.crop_ends_redefine_perc
+ #for $s in $cleaning_options.crop_ends_cond.crop_ends_retain_seqs
+ --crop_ends_retain '$s.crop_ends_retain'
+ #end for
+ #for $s in $cleaning_options.crop_ends_cond.crop_ends_retain_strings
+ --crop_ends_retain_str '$s.crop_ends_retain_str'
+ #end for
+ #end if
+
+ ### Remove Short options
+ #if str($cleaning_options.remove_short_cond.remove_short_param) == "true":
+ --remove_short
+ --remove_min_length $cleaning_options.remove_short_cond.remove_min_length
+ #for $s in $cleaning_options.remove_short_cond.remove_short_retain_seqs
+ --remove_short_retain '$s.remove_short_retain'
+ #end for
+ #for $s in $cleaning_options.remove_short_cond.remove_short_retain_strings
+ --remove_short_retain_str '$s.remove_short_retain_str'
+ #end for
+ #end if
+
+ ### Crop Divergent options
+ #if str($cleaning_options.crop_divergent_cond.crop_divergent_param) == "true":
+ --crop_divergent
+ --crop_divergent_min_prop_ident $cleaning_options.crop_divergent_cond.crop_divergent_min_prop_ident
+ --crop_divergent_min_prop_nongap $cleaning_options.crop_divergent_cond.crop_divergent_min_prop_nongap
+ --crop_divergent_buffer_size $cleaning_options.crop_divergent_cond.crop_divergent_buffer_size
+ #end if
+
+ ### Retain options
+ #if str($cleaning_options.retain_cond.retain_param) == "true":
+ #for $s in $cleaning_options.retain_cond.retain_seqs
+ --retain '$s.retain'
+ #end for
+ #for $s in $cleaning_options.retain_cond.retain_strings
+ --retain_str '$s.retain_str'
+ #end for
+ #end if
+
+ ### Keep Gap only
+ $cleaning_options.keep_gaponly
+
+ ###### Visualisation Options
+ ### basic visualisation options
+ $visualisation_options.basic_visualisation_options.plot_input
+ $visualisation_options.basic_visualisation_options.plot_output
+ $visualisation_options.basic_visualisation_options.plot_markup
+ $visualisation_options.basic_visualisation_options.plot_consensus_identity
+ $visualisation_options.basic_visualisation_options.plot_consensus_similarity
+ #if str($visualisation_options.output_settings_cond.output_settings_param) == "true":
+ --plot_width $visualisation_options.basic_visualisation_options.output_settings_cond.plot_width
+ --plot_height $visualisation_options.basic_visualisation_options.output_settings_cond.plot_height
+ --plot_dpi $visualisation_options.basic_visualisation_options.output_settings_cond.plot_dpi
+ $visualisation_options.basic_visualisation_options.output_settings_cond.plot_keep_numbers
+ $visualisation_options.basic_visualisation_options.output_settings_cond.plot_force_numbers
+ --plot_identity_palette '$visualisation_options.basic_visualisation_options.output_settings_cond.plot_identity_palette'
+ --plot_identity_gap_col '$visualisation_options.basic_visualisation_options.output_settings_cond.plot_identity_gap_col'
+ --plot_similarity_palette '$visualisation_options.basic_visualisation_options.output_settings_cond.plot_similarity_palette'
+ --plot_similarity_gap_col '$visualisation_options.basic_visualisation_options.output_settings_cond.plot_similarity_gap_col'
+ --plot_sub_matrix_name '$visualisation_options.basic_visualisation_options.output_settings_cond.plot_sub_matrix_name'
+ --palette '$visualisation_options.basic_visualisation_options.output_settings_cond.palette'
+ #end if
+
+ ### Sequence logos
+ #if str($visualisation_options.sequence_logo_cond.sequence_logo_param) == "true":
+ --make_sequence_logo
+ --sequence_logo_type "$visualisation_options.sequence_logo_cond.sequence_logo_type"
+ --sequence_logo_dpi $visualisation_options.sequence_logo_cond.sequence_logo_dpi
+ --sequence_logo_font '$visualisation_options.sequence_logo_cond.sequence_logo_font'
+ --sequence_logo_nt_per_row $visualisation_options.sequence_logo_cond.sequence_logo_nt_per_row
+ #if $visualisation_options.sequence_logo_cond.logo_start:
+ --logo_start $visualisation_options.sequence_logo_cond.logo_start
+ #end if
+ #if $visualisation_options.sequence_logo_cond.logo_end:
+ --logo_end $visualisation_options.sequence_logo_cond.logo_end
+ #end if
+ #end if
+
+ ### Statistics Plots
+ $visualisation_options.statistics_plots.plot_stats_input
+ $visualisation_options.statistics_plots.plot_stats_output
+ #if $visualisation_options.statistics_plots.plot_stats_input or $visualisation_options.statistics_plots.plot_stats_output
+ --plot_stats_dpi $visualisation_options.statistics_plots.stats_settings.plot_stats_dpi
+ --plot_stats_height $visualisation_options.statistics_plots.stats_settings.plot_stats_width
+ --plot_stats_width $visualisation_options.statistics_plots.stats_settings.plot_stats_height
+ --plot_stats_colour '$visualisation_options.statistics_plots.stats_settings.plot_stats_colour'
+ #end if
+
+ ###### Interpretation Functions
+ ### consensus sequences
+ #if str($interpretation_options.consensus_sequences_cond.consensus_sequences_param) == "true":
+ --make_consensus
+ --consensus_type '$interpretation_options.consensus_sequences_cond.consensus_type'
+ $interpretation_options.consensus_sequences_cond.consensus_keep_gaps
+ #end if
+
+ ### Position Matrices
+ $interpretation_options.position_matrices.pwm_input
+ $interpretation_options.position_matrices.pwm_output
+ #if $interpretation_options.position_matrices.matrices_settings.pwm_start:
+ --pwm_start $interpretation_options.position_matrices.matrices_settings.pwm_start
+ #end if
+ #if $interpretation_options.position_matrices.matrices_settings.pwm_end:
+ --pwm_end $interpretation_options.position_matrices.matrices_settings.pwm_end
+ #end if
+ #if $interpretation_options.position_matrices.pwm_input or $interpretation_options.position_matrices.pwm_output:
+ --pwm_freqtype '$interpretation_options.position_matrices.matrices_settings.pwm_freqtype'
+ --pwm_alphatype '$interpretation_options.position_matrices.matrices_settings.pwm_alphatype'
+ --pwm_alphaval $interpretation_options.position_matrices.matrices_settings.pwm_alphaval
+ #end if
+ $interpretation_options.position_matrices.pwm_output_blamm
+ $interpretation_options.position_matrices.pwm_output_meme
+
+ ### Similarity Matrices
+ $interpretation_options.similarity_matrices.make_similarity_matrix_input
+ $interpretation_options.similarity_matrices.make_similarity_matrix_output
+ #if $interpretation_options.similarity_matrices.make_similarity_matrix_input or $interpretation_options.similarity_matrices.make_similarity_matrix_output:
+ --make_simmatrix_keepgaps $interpretation_options.similarity_matrices.similarity_matrices_settings.make_simmatrix_keepgaps
+ --make_simmatrix_dp $interpretation_options.similarity_matrices.similarity_matrices_settings.make_simmatrix_dp
+ --make_simmatrix_minoverlap $interpretation_options.similarity_matrices.similarity_matrices_settings.make_simmatrix_minoverlap
+ #end if
+
+
+ ###### Editing Functions
+ #if str($editing_functions.get_section_cond.get_section_param) == "true":
+ --get_section
+ --section_start $editing_functions.get_section_cond.section_start
+ --section_end $editing_functions.get_section_cond.section_end
+ #end if
+ $editing_functions.replace_input_tu
+ $editing_functions.replace_input_ut
+ $editing_functions.replace_output_tu
+ $editing_functions.replace_output_ut
+ ### Unaligning
+ $editing_functions.unalign_input
+ $editing_functions.unalign_output
+ ### Removing Duplicates
+ $editing_functions.deduplicate_ids
+ #if str($editing_functions.deduplicate_ids)
+ --duporder '$editing_functions.duporder'
+ #end if
+ ]]>
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+ ^[a-zA-Z_]+$
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+ ^[a-zA-Z_]+$
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+ basic_options['log_out']
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+ visualisation_options['basic_visualisation_options']['plot_input'] or basic_options['visualise'] or basic_options['all']
+
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+ visualisation_options['basic_visualisation_options']['plot_output'] or basic_options['visualise'] or basic_options['all']
+
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+ visualisation_options['basic_visualisation_options']['plot_markup'] or basic_options['visualise'] or basic_options['all']
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+ visualisation_options['basic_visualisation_options']['plot_markup'] or basic_options['visualise'] or basic_options['all']
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+ visualisation_options['basic_visualisation_options']['plot_consensus_identity'] or basic_options['all']
+
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+ visualisation_options['basic_visualisation_options']['plot_consensus_similarity']
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+ (visualisation_options['sequence_logo_cond']['sequence_logo_param'] == 'true' and (visualisation_options['sequence_logo_cond']['sequence_logo_type'] == 'bar' or visualisation_options['sequence_logo_cond']['sequence_logo_type'] == 'both'))
+
+
+ (visualisation_options['sequence_logo_cond']['sequence_logo_param'] == 'true' and (visualisation_options['sequence_logo_cond']['sequence_logo_type'] == 'text' or visualisation_options['sequence_logo_cond']['sequence_logo_type'] == 'both'))
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+ visualisation_options['statistics_plots']['plot_stats_input'] or basic_options['interpret'] or basic_options['all']
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+ visualisation_options['statistics_plots']['plot_stats_output'] or basic_options['interpret'] or basic_options['all']
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+ interpretation_options['consensus_sequences_cond']['consensus_sequences_param'] == 'true' or basic_options['interpret'] or basic_options['all']
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+ interpretation_options['consensus_sequences_cond']['consensus_sequences_param'] == 'true' or basic_options['interpret'] or basic_options['all']
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+ interpretation_options['position_matrices']['pwm_input']
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+ interpretation_options['position_matrices']['pwm_input']
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+ interpretation_options['position_matrices']['pwm_input']
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+ interpretation_options['position_matrices']['pwm_input'] and interpretation_options['position_matrices']['pwm_output_meme']
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+ interpretation_options['position_matrices']['pwm_input'] and interpretation_options['position_matrices']['pwm_output_blamm']
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+ interpretation_options['position_matrices']['pwm_output']
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+ interpretation_options['position_matrices']['pwm_output']
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+ interpretation_options['position_matrices']['pwm_output']
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+ interpretation_options['position_matrices']['pwm_output'] and interpretation_options['position_matrices']['pwm_output_meme']
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+ interpretation_options['position_matrices']['pwm_output'] and interpretation_options['position_matrices']['pwm_output_blamm']
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+ interpretation_options['similarity_matrices']['make_similarity_matrix_input'] or basic_options['interpret'] or basic_options['all']
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+ interpretation_options['similarity_matrices']['make_similarity_matrix_output'] or basic_options['interpret'] or basic_options['all']
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+ basic_options['interpret'] or basic_options['all']
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+ basic_options['interpret'] or basic_options['all']
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+ editing_functions['replace_input_tu']
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+ editing_functions['replace_input_ut']
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+ editing_functions['replace_output_tu']
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+ editing_functions['replace_output_ut']
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+ editing_functions['unalign_input']
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+ editing_functions['unalign_output']
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diff -r 000000000000 -r 9dce901753b9 macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Mon Mar 02 15:36:38 2026 +0000
@@ -0,0 +1,43 @@
+
+ 1.1.4
+ 1
+
+
+ cialign
+
+
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+
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+
+ 10.7717/peerj.12983
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+
\ No newline at end of file
diff -r 000000000000 -r 9dce901753b9 test-data/example1.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/example1.fasta Mon Mar 02 15:36:38 2026 +0000
@@ -0,0 +1,14 @@
+>Seq1
+AGUCUAUCUGGGGUACUAUCUA------UCGCUACGUACUAGCUUACGUACUGACUUA--CGCUACGUACUAGCUUACGUACUGACUUA-------
+>Seq2
+AUUCUAUCUGGGUGACUAUUCG------UUAUCUCUACUUACUAUCUUACUUACUUACUUACGCUACGUACUAGCUUACGUACUGACUU-------
+>Seq3
+AUUCUAUCUGGGUACUAUUGGGCUCUUAUUAUCUCUACUUACUAUCUUACUUACUUACUUACGCUACGUACUAGCUUACGUACUGACUU-------
+>Seq4
+AUUCUAUCUGGGUACUAUUGGG------UUAAGCUAUACUUUAGGAACAAAAUCUUACUUACGCUACGUACUAGCUUACGUACUGACUU-------
+>Seq5
+AUUCUAUCUGGGUACUAUUGGG------UUAUCUCUACUUACUAUCUUACUUACUUACUUA-------------------------------AAAA
+>Seq6
+AUUCUAUC------UAUUGG--------UUAUCU--------------------------------------------------------------
+>Seq7
+AUUCUAUCUGGGUACUAUUGGG------UUAUCUCUACUUACUAUCUUACAGACUUGGUUA-------------------------------AAAA
\ No newline at end of file
diff -r 000000000000 -r 9dce901753b9 test-data/example2.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/example2.fasta Mon Mar 02 15:36:38 2026 +0000
@@ -0,0 +1,6 @@
+>seq1
+MKT--AIKDLGTEYKLTVAEYFR
+>seq2
+MKTGAIKDL-T-EYKL-VAEYFR
+>seq3
+MKTGAIKDLGTEYKLT-AA-YFR
\ No newline at end of file
diff -r 000000000000 -r 9dce901753b9 test-data/example3.fasta.gz
Binary file test-data/example3.fasta.gz has changed