| Previous changeset 0:2595c27071c2 (2020-02-15) Next changeset 2:98099e4da1fd (2024-06-14) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kma commit a3fc5e6a1731ed2a63aed6b4c3e858bf4d9beecd" |
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modified:
kma_map.xml |
| b |
| diff -r 2595c27071c2 -r 95ab864b281a kma_map.xml --- a/kma_map.xml Sat Feb 15 15:32:58 2020 -0500 +++ b/kma_map.xml Sat Nov 27 09:36:00 2021 +0000 |
| [ |
| b'@@ -1,4 +1,4 @@\n-<tool id="kma_map" name="Map with KMA" version="@TOOL_VERSION@+galaxy0">\n+<tool id="kma_map" name="Map with KMA" version="@TOOL_VERSION@+galaxy1">\n <description></description>\n <macros>\n <import>macros.xml</import>\n@@ -11,7 +11,7 @@\n <![CDATA[\n kma\n -t \\${GALAXY_SLOTS:-1}\n-\t -t_db \'${kma_index.fields.path}\'\n+ -t_db \'${kma_index.fields.path}\'\n #if $single_paired.single_paired_selector == \'paired\'\n -ipe \'${single_paired.forward_input}\' \'${single_paired.reverse_input}\'\n #elif $single_paired.single_paired_selector == "paired_collection":\n@@ -26,6 +26,7 @@\n #if str($settings.p_value)\n -p \'${settings.p_value}\'\n #end if\n+ $settings.exhaustive_mode\n ${settings.decontaminate}\n ${settings.dense}\n ${settings.ref_fsa}\n@@ -60,12 +61,13 @@\n -gapextend \'${settings.gapextend}\'\n #end if\n ${settings.force_end_to_end}\n+ -per $settings.pairing_reward\n ${settings.set_cge_penalties_and_rewards}\n #end if\n -o output\n \t \n #if str($settings.advanced) == "advanced" and $settings.matrix\n- && gunzip output.mat.gz\n+ && gunzip output.mat.gz\n #end if\n && gunzip output.frag.gz\n \t]]>\n@@ -78,17 +80,17 @@\n <option selected="True" value="single">Single-end data</option>\n </param>\n <when value="paired_collection">\n- <param format="@INTYPES@" name="input_pair" type="data_collection" collection_type="paired" label="Collection of paired reads" help="FASTQ datasets" />\n+ <param argument="-ipe" format="@INTYPES@" name="input_pair" type="data_collection" collection_type="paired" label="Collection of paired reads" help="FASTQ datasets" />\n </when>\n <when value="paired">\n- <param format="@INTYPES@" name="forward_input" type="data" label="Forward strand" help="FASTQ dataset"/>\n- <param format="@INTYPES@" name="reverse_input" type="data" label="Reverse strand" help="FASTQ dataset"/>\n+ <param argument="-ipe" format="@INTYPES@" name="forward_input" type="data" label="Forward strand" help="FASTQ dataset"/>\n+ <param argument="-ipe" format="@INTYPES@" name="reverse_input" type="data" label="Reverse strand" help="FASTQ dataset"/>\n </when>\n <when value="single">\n- <param format="@INTYPES@" label="Input sequences" name="input_sequences" type="data" help="FASTQ datasets"/>\n+ <param argument="-i" format="@INTYPES@" label="Input sequences" name="input_sequences" type="data" help="FASTQ datasets"/>\n </when>\n </conditional>\n- <param name="kma_index" type="select">\n+ <param argument="-t_db" name="kma_index" type="select">\n <options from_data_table="kma_index">\n <validator type="no_options" message="No KMA index available" />\n </options>\n@@ -101,27 +103,27 @@\n <when value="simple">\n </when>\n <when value="advanced">\n- <param name="kmer_size" type="integer" min="4" value="16" max="32" label="Kmer Size" />\n- <param name="p_value" type="float" min="0.0" value="0.05" max="1.0" label="p-value"/>\n- <param name="exhaustive_mode" type="boolean" truevalue="-ex_mode" falsevalue="" label="Exhaustive Mode" />\n- <param name="decontaminate" type="boolean" truevalue="-deCon" falsevalue="" label="Decontaminate" />\n- <param name="dense" type="boolean" truevalue="-dense" falsevalue="" label="Do not allow insertions in assembly" />\n- <param name="ref_fsa" type="boolean" truevalue="-ref_fsa" falsevalue="" label="Consensus sequence has \'n\' instead of gaps" />\n- '..b'_depth" type="integer" min="1" value="1" max="1000" label="Minimum depth at base" />\n- <param name="minimum_mapping_quality" type="integer" min="0" value="0" max="100" label="Minimum mapping quality" />\n- <param name="reward" type="integer" min="1" value="1" max="100" label="Score for match" />\n- <param name="penalty" type="integer" min="-100" value="-2" max="0" label="Penalty for mismatch" />\n- <param name="gapopen" type="integer" min="-100" value="-3" max="0" label="Penalty for gap opening" />\n- <param name="gapextend" type="integer" min="-100" value="-1" max="0" label="Penalty for gap extension" />\n- <param name="pairing_reward" type="integer" min="1" value="7" max="100" label="Reward for pairing reads" />\n- <param name="set_cge_penalties_and_rewards" type="boolean" truevalue="-cge" falsevalue="" label="Set CGE penalties and rewards" />\n+ <param argument="-k" name="kmer_size" type="integer" min="4" value="16" max="32" label="Kmer Size" />\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="-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+ <param argument="-Sparse" name="only_count_kmers" type="boolean" truevalue="-Sparse" falsevalue="" label="Only count kmers" />\n+ <param argument="-ID" name="min_id" type="float" min="0.0" value="1.0" max="100.0" label="Minimum percent identity"/>\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="-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' |