Mercurial > repos > galaxy-australia > kmc
diff kmc_tools_simple.xml @ 0:ca2743037241 draft default tip
"planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
| author | galaxy-australia |
|---|---|
| date | Tue, 27 Sep 2022 05:20:06 +0000 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/kmc_tools_simple.xml Tue Sep 27 05:20:06 2022 +0000 @@ -0,0 +1,425 @@ +<tool id="kmc_simple" name="KMC simple" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" > + <description>simple operations for two input kmer sets</description> + <xrefs> + <xref type='bio.tools'>kmc</xref> + </xrefs> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <expand macro="stdio" /> + <expand macro="version_command" /> + <command><![CDATA[ + mkdir outdir && + #for $f in $input_collection_one: + #if '.kmc_suf' in str($f.element_identifier) + ln -s '${f}' kmers_db_one.kmc_suf && + #else + ln -s '${f}' kmers_db_one.kmc_pre && + #end if + #end for + #for $f in $input_collection_two: + #if '.kmc_suf' in str($f.element_identifier) + ln -s '${f}' kmers_db_two.kmc_suf && + #else + ln -s '${f}' kmers_db_two.kmc_pre && + #end if + #end for + kmc_tools + -t\${GALAXY_SLOTS:-4} + simple + #if $input_options_cond.input_param == "None": + kmers_db_one + kmers_db_two + #elif $input_options_cond.input_param == "kmc_one_params": + kmers_db_one + -ci'$input_options_cond.kmc_db_one_param.min_kmer_occurrence' + -cx'$input_options_cond.kmc_db_one_param.max_kmer_occurrence' + kmers_db_two + #elif $input_options_cond.input_param == "kmc_two_params": + kmers_db_one + kmers_db_two + -ci'$input_options_cond.kmc_db_two_param.min_kmer_occurrence' + -cx'$input_options_cond.kmc_db_two_param.max_kmer_occurrence' + #elif $input_options_cond.input_param == "both_kmc_params": + kmers_db_one + -ci'$input_options_cond.both_db_one_param.min_kmer_occurrence' + -cx'$input_options_cond.both_db_one_param.max_kmer_occurrence' + kmers_db_two + -ci'$input_options_cond.both_db_two_param.min_kmer_occurrence' + -cx'$input_options_cond.both_db_two_param.max_kmer_occurrence' + #end if + #set $operation_arr=[] + #for $i,$opt in enumerate($operations) + #silent $operation_arr.append(str($opt.ops.select_operation)) + #if str($opt.ops.select_operation) == "intersect": + $opt.ops.select_operation + #if str($opt.ops.add_output_params.oc) != 'None': + '${opt.ops.select_operation}_${opt.ops.add_output_params.oc}_db' + -oc'$opt.ops.add_output_params.oc' + #else + '${opt.ops.select_operation}_min_db' + -oc'min' + #end if + #if str($opt.ops.add_output_params.min_kmer_occurrence) != '': + -ci'$opt.ops.add_output_params.min_kmer_occurrence' + #end if + #if str($opt.ops.add_output_params.max_kmer_occurrence) != '': + -cx'$opt.ops.add_output_params.max_kmer_occurrence' + #end if + #elif str($opt.ops.select_operation) == "union": + $opt.ops.select_operation + #if str($opt.ops.add_output_params.oc) != 'None': + '${opt.ops.select_operation}_${opt.ops.add_output_params.oc}_db' + -oc'$opt.ops.add_output_params.oc' + #else + '${opt.ops.select_operation}_sum_db' + -oc'sum' + #end if + #if str($opt.ops.add_output_params.min_kmer_occurrence) != '': + -ci'$opt.ops.add_output_params.min_kmer_occurrence' + #end if + #if str($opt.ops.add_output_params.max_kmer_occurrence) != '': + -cx'$opt.ops.add_output_params.max_kmer_occurrence' + #end if + #elif str($opt.ops.select_operation) == "kmers_subtract": + $opt.ops.select_operation + ${opt.ops.select_operation}_db + #if str($opt.ops.add_output_params.min_kmer_occurrence) != '': + -ci'$opt.ops.add_output_params.min_kmer_occurrence' + #end if + #if str($opt.ops.add_output_params.max_kmer_occurrence) != '': + -cx'$opt.ops.add_output_params.max_kmer_occurrence' + #end if + #elif str($opt.ops.select_operation) == "reverse_kmers_subtract": + $opt.ops.select_operation + ${opt.ops.select_operation}_db + #if str($opt.ops.add_output_params.min_kmer_occurrence) != '': + -ci'$opt.ops.add_output_params.min_kmer_occurrence' + #end if + #if str($opt.ops.add_output_params.max_kmer_occurrence) != '': + -cx'$opt.ops.add_output_params.max_kmer_occurrence' + #end if + #elif str($opt.ops.select_operation) == "counters_subtract": + $opt.ops.select_operation + #if str($opt.ops.add_output_params.oc) != 'None': + '${opt.ops.select_operation}_${opt.ops.add_output_params.oc}_db' + -oc'$opt.ops.add_output_params.oc' + #else + '${opt.ops.select_operation}_min_db' + -oc'diff' + #end if + #if str($opt.ops.add_output_params.min_kmer_occurrence) != '': + -ci'$opt.ops.add_output_params.min_kmer_occurrence' + #end if + #if str($opt.ops.add_output_params.max_kmer_occurrence) != '': + -cx'$opt.ops.add_output_params.max_kmer_occurrence' + #end if + #elif str($opt.ops.select_operation) == "reverse_counters_subtract": + $opt.ops.select_operation + #if str($opt.ops.add_output_params.oc) != 'None': + '${opt.ops.select_operation}_${opt.ops.add_output_params.oc}_db' + -oc'$opt.ops.add_output_params.oc' + #else + '${opt.ops.select_operation}_min_db' + -oc'diff' + #end if + #if str($opt.ops.add_output_params.min_kmer_occurrence) != '': + -ci'$opt.ops.add_output_params.min_kmer_occurrence' + #end if + #if str($opt.ops.add_output_params.max_kmer_occurrence) != '': + -cx'$opt.ops.add_output_params.max_kmer_occurrence' + #end if + #end if + #end for + + #for $i,$op in enumerate($operation_arr): + #if str($op) == "kmers_subtract" or str($op) == "reverse_kmers_subtract": + && cp '${op}'_db.kmc_suf outdir/ + && cp '${op}'_db.kmc_pre outdir/ + 2>&1 | tee -a '$out_log' + #else + && cp '${op}'_*_db.kmc_suf outdir/ + && cp '${op}'_*_db.kmc_pre outdir/ + 2>&1 | tee -a '$out_log' + #end if + #end for + ]]></command> + <inputs> + <param name="input_collection_one" type="data_collection" collection_type="list" label="KMC db one"/> + <param name="input_collection_two" type="data_collection" collection_type="list" label="KMC db two"/> + <conditional name="input_options_cond"> + <param name="input_param" type="select" label="Input parameters"> + <option value="None" selected="true">Both KMC DB with default parameters</option> + <option value="kmc_one_params">KMC db one only</option> + <option value="kmc_two_params">KMC db two only</option> + <option value="both_kmc_params">Both KMC DB with user parameters</option> + </param> + <when value="None"/> + <when value="kmc_one_params"> + <section name="kmc_db_one_param" title="KMC DB one parameters"> + <expand macro="input_option"/> + </section> + </when> + <when value="kmc_two_params"> + <section name="kmc_db_two_param" title="KMC DB two parameters"> + <expand macro="input_option"/> + </section> + </when> + <when value="both_kmc_params"> + <section name="both_db_one_param" title="KMC DB one parameters"> + <expand macro="input_option"/> + </section> + <section name="both_db_two_param" title="KMC DB two parameters"> + <expand macro="input_option"/> + </section> + </when> + </conditional> + <repeat name="operations" title="Operations" min="1" max="3"> + <conditional name="ops"> + <expand macro="simple_operation"/> + <when value="intersect"> + <section name="add_output_params" expanded="false" title="Additional output parameters"> + <expand macro="counter_calculation_option"/> + </section> + </when> + <when value="union"> + <section name="add_output_params" expanded="false" title="Additional output parameters"> + <expand macro="counter_calculation_option"/> + </section> + </when> + <when value="kmers_subtract"> + <section name="add_output_params" expanded="false" title="Additional output parameters"> + <expand macro="none_counter_calculation_option"/> + </section> + </when> + <when value="reverse_kmers_subtract"> + <section name="add_output_params" expanded="false" title="Additional output parameters"> + <expand macro="none_counter_calculation_option"/> + </section> + </when> + <when value="counters_subtract"> + <section name="add_output_params" expanded="false" title="Additional output parameters"> + <expand macro="counter_calculation_option"/> + </section> + </when> + <when value="reverse_counters_subtract"> + <section name="add_output_params" expanded="false" title="Additional output parameters"> + <expand macro="counter_calculation_option"/> + </section> + </when> + </conditional> + </repeat> + </inputs> + <outputs> + <collection name="kmc_db" type="list" label="${tool.name} on ${on_string}: kmc db"> + <discover_datasets pattern="(?P<designation>.+)" format="binary" directory="outdir/" /> + </collection> + <data name="out_log" format="txt" label="${tool.name} on ${on_string}: log"/> + </outputs> + <tests> + <test> + <!-- #1 test with default parameters --> + <param name="input_collection_one"> + <collection type="list"> + <element name="kmers_one.kmc_suf" value="kmers_one.kmc_suf"/> + <element name="kmers_one.kmc_pre" value="kmers_one.kmc_pre"/> + </collection> + </param> + <param name="input_collection_two"> + <collection type="list"> + <element name="kmers_two.kmc_suf" value="kmers_two.kmc_suf"/> + <element name="kmers_two.kmc_pre" value="kmers_two.kmc_pre"/> + </collection> + </param> + <conditional name="input_options_cond"> + <param name="input_param" value="None"/> + </conditional> + <param name="select_operation" value="intersect" /> + <section name="add_output_params"> + <param name="oc" value="max"/> + </section> + <output_collection name="kmc_db" type="list"> + <element name="intersect_max_db.kmc_suf" file="intersect_max_db.kmc_suf"/> + <element name="intersect_max_db.kmc_pre" file="intersect_max_db.kmc_pre"/> + </output_collection> + </test> + <test> + <!-- #2 test with input parameters for KMC DB one only --> + <param name="input_collection_one"> + <collection type="list"> + <element name="kmers_one.kmc_suf" value="kmers_one.kmc_suf"/> + <element name="kmers_one.kmc_pre" value="kmers_one.kmc_pre"/> + </collection> + </param> + <param name="input_collection_two"> + <collection type="list"> + <element name="kmers_two.kmc_suf" value="kmers_two.kmc_suf"/> + <element name="kmers_two.kmc_pre" value="kmers_two.kmc_pre"/> + </collection> + </param> + <conditional name="input_options_cond"> + <param name="input_param" value="kmc_one_params"/> + </conditional> + <param name="select_operation" value="intersect" /> + <section name="kmc_db_one_param"> + <param name="min_kmer_occurrence" value="3"/> + <param name="max_kmer_occurrence" value="30"/> + </section> + <section name="add_output_params"> + <param name="oc" value="min"/> + </section> + <output_collection name="kmc_db" type="list"> + <element name="intersect_min_db.kmc_suf" file="intersect_min_db.kmc_suf"/> + <element name="intersect_min_db.kmc_pre" file="intersect_min_db.kmc_pre"/> + </output_collection> + </test> + <test> + <!-- #3 test with input parameters for KMC DB two only --> + <param name="input_collection_one"> + <collection type="list"> + <element name="kmers_one.kmc_suf" value="kmers_one.kmc_suf"/> + <element name="kmers_one.kmc_pre" value="kmers_one.kmc_pre"/> + </collection> + </param> + <param name="input_collection_two"> + <collection type="list"> + <element name="kmers_two.kmc_suf" value="kmers_two.kmc_suf"/> + <element name="kmers_two.kmc_pre" value="kmers_two.kmc_pre"/> + </collection> + </param> + <conditional name="input_options_cond"> + <param name="input_param" value="kmc_two_params"/> + </conditional> + <param name="select_operation" value="union" /> + <section name="kmc_db_two_param"> + <param name="min_kmer_occurrence" value="3"/> + <param name="max_kmer_occurrence" value="30"/> + </section> + <output_collection name="kmc_db" type="list"> + <element name="union_db.kmc_suf" file="union_db.kmc_suf"/> + <element name="union_db.kmc_pre" file="union_db.kmc_pre"/> + </output_collection> + </test> + <test> + <!-- #4 test with input parameters for both KMC DB --> + <param name="input_collection_one"> + <collection type="list"> + <element name="kmers_one.kmc_suf" value="kmers_one.kmc_suf"/> + <element name="kmers_one.kmc_pre" value="kmers_one.kmc_pre"/> + </collection> + </param> + <param name="input_collection_two"> + <collection type="list"> + <element name="kmers_two.kmc_suf" value="kmers_two.kmc_suf"/> + <element name="kmers_two.kmc_pre" value="kmers_two.kmc_pre"/> + </collection> + </param> + <conditional name="input_options_cond"> + <param name="input_param" value="both_kmc_params"/> + </conditional> + <param name="select_operation" value="counters_subtract" /> + <section name="both_db_one_param"> + <param name="min_kmer_occurrence" value="2"/> + <param name="max_kmer_occurrence" value="20"/> + </section> + <section name="both_db_two_param"> + <param name="min_kmer_occurrence" value="3"/> + <param name="max_kmer_occurrence" value="30"/> + </section> + <section name="add_output_params"> + <param name="oc" value="sum"/> + </section> + <output_collection name="kmc_db" type="list"> + <element name="counters_subtract_sum_db.kmc_suf" file="counters_subtract_sum_db.kmc_suf"/> + <element name="counters_subtract_sum_db.kmc_pre" file="counters_subtract_sum_db.kmc_pre"/> + </output_collection> + </test> + </tests> + <help><![CDATA[ + +.. class:: infomark + + +**What it does** + +*KMC simple operation performs set operation on two input KMC's databases* + +**General Syntax** + +kmc_tools simple <input1 [input1_params]> <input2 [input2_params]> <oper1 output1 [output_params1]> [<oper2 output2 [output_params2]> ...] + +**Input:** + +- input file - input1 and input2 are the databases generated by KMC ( kmc file suffix - kmc_pre and kmc_suf ) + +**Available Operations:** + +- intersect - output database will contains only k-mers that are present in both input sets +- union - output database will contains each k-mer present in any of input sets +- kmers_subtract - difference of input sets based on k-mers. Output database will contains only k-mers that are present in first input set but absent in the second one +- counters_subtract - difference of input sets based on k-mers and their counters (weaker version of kmers_subtract). Output database will contains all k-mers that are present in first input, beyond those for which counter operation will lead to remove (i.e. counter equal to 0 or negative number) +- reverse_kmers_subtract - same as kmers_subtract but treat input2 as first and input1 as second +- reverse_counters_subtract - same as counters_subtract but treat input2 as first and input1 as second + +**Additional Parameters for inputs:** + +- ci<value> - exclude k-mers occurring less than <value> times +- cx<value> - exclude k-mers occurring more of than <value> times + +**Additional Parameters for outputs:** + +- ci<value> - exclude k-mers occurring less than <value> times +- cx<value> - exclude k-mers occurring more of than <value> times +- cs<value> - maximal value of a counter +- o<kmc|kff> - output in KMC or KFF format (default: kmc) +- oc<value> - redefine counter calculation mode for equal k-mers + +**Available oc<value>** + +- min - get lower value of a k-mer counter (default value for intersect operation) +- max - get upper value of a k-mer counter +- sum - get sum of counters from both databases +- diff - get difference between counters (default for counters_subtract operation) +- left - get counter from first database (input1) +- right - get counter from second database (input2) + + +**Example(1):** + +- kmc -k27 file1.fastq kmers1 kmc_tmp_dir +- kmc -k27 file2.fastq kmers2 kmc_tmp_dir +- kmc_tools simple kmers1 -ci10 -cx200 kmers2 -ci4 -cx100 intersect kmers1_kmers2_intersect -ci20 -cx150 + +**Output(1)** + +- kmers1_kmers2_intersect.kmc_suf (i.e intersect_kmc_suf in galaxy) +- kmers1_kmers2_intersect.kmc_pre (i.e intersect_kmc_pre in galaxy) + +**Example(2):** + +- kmc -k27 file1.fastq kmers1 kmc_tmp_dir +- kmc -k27 file2.fastq kmers2 kmc_tmp_dir +- kmc_tools simple kmers1 kmers2 intersect inter_k1_k2_max -ocmax intersect inter_k1_k2_min union union_k1_k2 -ci10 + +**Output(2)** + +- inter_k1_k2_max.kmc_suf (i.e intersect.kmc_suf in galaxy) +- inter_k1_k2_max.kmc_pre (i.e intersect.kmc_pre in galaxy) +- inter_k1_k2_min.kmc_suf (i.e intersect.kmc_suf in galaxy) +- inter_k1_k2_min.kmc_pre (i.e intersect.kmc_pre in galaxy) +- union_k1_k2.kmc_suf (i.e union.kmc_suf in galaxy) +- union_k1_k2.kmc_pre (i.e union.kmc_pre in galaxy + +.. class:: infomark + +**References** + +More information are available on `website <https://github.com/refresh-bio/KMC/blob/master/kmc_tools.pdf>`_. + ]]></help> + <citations> + <citation type="doi">DOI: 10.1093/bioinformatics/btx304</citation> + <citation type="doi">DOI: 10.1093/bioinformatics/btv022</citation> + <citation type="doi">DOI: 10.1186/1471-2105-14-160</citation> + </citations> +</tool>