| Previous changeset 1:95ab864b281a (2021-11-27) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kma commit 812bb0a31f030096bf1b0836f64e76b820c8e2c2 |
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modified:
kma_map.xml macros.xml |
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| diff -r 95ab864b281a -r 98099e4da1fd kma_map.xml --- a/kma_map.xml Sat Nov 27 09:36:00 2021 +0000 +++ b/kma_map.xml Fri Jun 14 21:15:44 2024 +0000 |
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| b'@@ -1,4 +1,4 @@\n-<tool id="kma_map" name="Map with KMA" version="@TOOL_VERSION@+galaxy1">\n+<tool id="kma_map" name="Map with KMA" version="@TOOL_VERSION@+galaxy0" profile="23.0">\n <description></description>\n <macros>\n <import>macros.xml</import>\n@@ -107,9 +107,9 @@\n <param argument="-p" name="p_value" type="float" min="0.0" value="0.05" max="1.0" label="p-value"/>\n <param argument="-ex_mode" name="exhaustive_mode" type="boolean" truevalue="-ex_mode" falsevalue="" label="Exhaustive Mode" />\n <param argument="-deCon" name="decontaminate" type="boolean" truevalue="-deCon" falsevalue="" label="Decontaminate" />\n- <param argument="-dense" name="dense" type="boolean" truevalue="-dense" falsevalue="" label="Do not allow insertions in assembly" />\n- <param argument="-ref_fsa" name="ref_fsa" type="boolean" truevalue="-ref_fsa" falsevalue="" label="Consensus sequence has \'n\' instead of gaps" />\n- <param argument="-matrix" name="matrix" type="boolean" truevalue="-matrix" falsevalue="" label="Output assembly matrix" />\n+ <param argument="-dense" type="boolean" truevalue="-dense" falsevalue="" label="Do not allow insertions in assembly" />\n+ <param argument="-ref_fsa" type="boolean" truevalue="-ref_fsa" falsevalue="" label="Consensus sequence has \'n\' instead of gaps" />\n+ <param argument="-matrix" type="boolean" truevalue="-matrix" falsevalue="" label="Output assembly matrix" />\n <param argument="-a" name="all_best_mappings" type="boolean" truevalue="-a" falsevalue="" label="Print all best mappings" />\n <param argument="-mp" name="minimum_phred_score" type="integer" min="0" value="20" max="60" label="Minimum phred score" />\n <param argument="-5p" name="cut_5_prime" type="integer" min="0" value="0" max="64" label="Cut a constant number of nucleotides from the 5 prime" />\n@@ -118,64 +118,96 @@\n <param argument="-1t1" name="force_end_to_end" type="boolean" truevalue="-1t1" falsevalue="" label="Force end to end mapping" />\n <param argument="-bcd" name="base_call_depth" type="integer" min="1" value="1" max="1000" label="Minimum depth at base" />\n <param argument="-mq" name="minimum_mapping_quality" type="integer" min="0" value="0" max="100" label="Minimum mapping quality" />\n- <param argument="-reward" name="reward" type="integer" min="1" value="1" max="100" label="Score for match" />\n- <param argument="-penalty" name="penalty" type="integer" min="-100" value="-2" max="0" label="Penalty for mismatch" />\n- <param argument="-gapopen " name="gapopen" type="integer" min="-100" value="-3" max="0" label="Penalty for gap opening" />\n- <param argument="-gapextend" name="gapextend" type="integer" min="-100" value="-1" max="0" label="Penalty for gap extension" />\n+ <param argument="-reward" type="integer" min="1" value="1" max="100" label="Score for match" />\n+ <param argument="-penalty" type="integer" min="-100" value="-2" max="0" label="Penalty for mismatch" />\n+ <param argument="-gapopen" type="integer" min="-100" value="-3" max="0" label="Penalty for gap opening" />\n+ <param argument="-gapextend" type="integer" min="-100" value="-1" max="0" label="Penalty for gap extension" />\n <param argument="-per" name="pairing_reward" type="integer" min="1" value="7" max="100" label="Reward for pairing reads" />\n <param argument="-cge" name="set_cge_penalties_and_rewards" type="boolean" truevalue="-cge" falsevalue="" label="Set CGE penalties and rewards" />\n </when>\n </conditional>\n </inputs>\n <outputs>\n- <data name="result_overview" label="Result overview" format="tabular" from_work_dir="output.res" />\n- <data name="consens'..b'output name="result_overview" file="ERR884056.res" ftype="tabular"/>\n- <output name="consensus_alignment" file="ERR884056.aln" ftype="fasta"/>\n- <output name="consensus_sequences" file="ERR884056.fsa" ftype="fasta"/>\n- <output name="read_mapping" file="ERR884056.frag" ftype="tabular"/>\n+ <output name="result_overview" ftype="tabular">\n+ <assert_contents>\n+ <has_n_lines n="3"/>\n+ <has_n_columns n="11"/>\n+ <has_text text="#Template"/>\n+ <has_text text="b0842_1"/>\n+ </assert_contents>\n+ </output>\n+ <output name="consensus_alignment" ftype="txt">\n+ <assert_contents>\n+ <has_n_lines n="170"/>\n+ <has_text text="b0842_1"/>\n+ <has_text text="query" n="42"/>\n+ <has_text text="template" n="42"/>\n+ </assert_contents>\n+ </output>\n+ <output name="consensus_sequences" ftype="fasta">\n+ <assert_contents>\n+ <has_line_matching expression="^>.*" n="2"/>\n+ <has_line_matching expression="^>b0842_1"/>\n+ </assert_contents>\n+ </output>\n+ <output name="read_mapping" ftype="tabular">\n+ <assert_contents>\n+ <has_n_lines n="492"/>\n+ <has_n_columns n="7"/>\n+ <has_text text="b0842_1"/>\n+ </assert_contents>\n+ </output>\n </test>\n- <test>\n+ <test expect_num_outputs="5">\n <param name="single_paired_selector" value="single"/>\n <param name="input_sequences" value="ERR884056_ecoli_b0842.mapped_R1.fastq" ftype="fastq"/>\n <param name="advanced" value="advanced"/>\n <param name="kmer_size" value="8"/>\n <param name="matrix" value="true"/>\n <param name="kma_index" value="test_index"/>\n- <output name="assembly_matrix" file="ERR884056.mat" ftype="txt"/>\n+ <output name="assembly_matrix" ftype="tabular">\n+ <assert_contents>\n+ <has_n_lines n="2553"/>\n+ <has_n_columns n="7" comment="#"/>\n+ <has_line_matching expression="^A	.*"/>\n+ <has_line_matching expression="^T	.*"/>\n+ <has_line_matching expression="^C	.*"/>\n+ <has_line_matching expression="^G	.*"/>\n+ </assert_contents>\n+ </output>\n </test>\n </tests>\n- <help>\n- <![CDATA[\n+ <help><![CDATA[\n \n When the mapping is done KMA will produce the following files:\n \n- *.res A result overview giving the most common statistics for each mapped template.\n- *.fsa The consensus sequences drawn from the alignments.\n- *.aln The consensus alignment of the reads against their template.\n- *.frag Mapping information on each mapped read, columns are: \n- 1. read\n- 2. number of equally well mapping templates\n- 3. mapping score\n- 4. start position\n- 5. end position (w.r.t. template)\n- 6. the choosen template.\n- *.mat Base counts on each position in each template, (only if \xe2\x80\x9c-matrix\xe2\x80\x9d is enabled)\n+* .res A result overview giving the most common statistics for each mapped template.\n+* .fsa The consensus sequences drawn from the alignments.\n+* .aln The consensus alignment of the reads against their template.\n+* .frag Mapping information on each mapped read, columns are: \n+ 1. read\n+ 2. number of equally well mapping templates\n+ 3. mapping score\n+ 4. start position\n+ 5. end position (w.r.t. template)\n+ 6. the choosen template.\n \n- ]]>\n- </help>\n+* .mat Base counts on each position in each template, (only if `-matrix` is enabled)\n+]]></help>\n <expand macro="citations" />\n </tool>\n' |
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| diff -r 95ab864b281a -r 98099e4da1fd macros.xml --- a/macros.xml Sat Nov 27 09:36:00 2021 +0000 +++ b/macros.xml Fri Jun 14 21:15:44 2024 +0000 |
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| @@ -1,5 +1,5 @@ <macros> - <token name="@TOOL_VERSION@">1.2.21</token> + <token name="@TOOL_VERSION@">1.4.14</token> <token name="@INTYPES@"> fastq,fastq.gz,fastqsanger,fastqsanger.gz </token> |