Mercurial > repos > epigenome > history_summary
changeset 0:11b4dfe32bc3 draft default tip
planemo upload for repository https://github.com/epigenome/galaxy-epigenome/tree/history/tools/history_summary commit 2e0a8a269e408eab18f8dbd67beed656f7694042
| author | epigenome |
|---|---|
| date | Sat, 09 Apr 2016 14:50:53 -0400 |
| parents | |
| children | |
| files | history_summary.xml |
| diffstat | 1 files changed, 360 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/history_summary.xml Sat Apr 09 14:50:53 2016 -0400 @@ -0,0 +1,360 @@ +<tool id="history_summary" name="HistorySummary" version="0.2"> + <description>generates a html for summarizing the current history contents along with renaming the output files</description> + <xml name="stdio"> + <stdio> + <exit_code range="1:" /> + </stdio> + </xml> + <command><![CDATA[ + #import re + #set global $gap = " " + ##set global $prefix = str($__app__.config.os_host) + #set global $prefix = $get_prefix($os.environ['PWD'] + '/' + $os.environ['GALAXY_CONFIG_FILE']) + + #def get_prefix(path) + #set $p = re.compile('^\s*prefix\s*=\s*(\S+)') + #set $file = open(path) + #for $line in $file + #set $m = $p.search($line) + #if $m + #return $m.group(1) + #end if + #end for + #return '' + #end def + + #def print_Dataset($ds, $ident) + echo "${ident}DS: '$ds.name' $ds.state $ds.deleted $ds.purged" $ds.get_file_name() >> $output; + #end def + + #def enum_DatasetCollection($dsc, $jobs) + #for $el in $dsc.elements + #if $el.hda + $enum_HistoryDatasetAssociation($el.hda, $jobs) + #elif $el.ldda + $enum_LibraryDatasetAssociation($el.ldda, $jobs) + #elif $el.child_collection + $enum_DatasetCollection($el.child_collection, $jobs) + #end if + #end for + #end def + + #def print_JobToDataAssociation($jda, $useName, $rules, $isOutput=False) + #if $jda.dataset + #set $buf = "<li>" + #if $useName + #set $buf += $jda.name + ": " + #end if + #set $buf += "<a href='" + $prefix + "/datasets/" + $__app__.security.encode_id($jda.dataset.id) + "/display?preview=True'><font color=black>" + #if $rules and $rules.has_key(str($jda.dataset.id)) + #set $file = $rules[str($jda.dataset.id)] + #else + #set $file = $jda.dataset.name + #end if + #if $isOutput and $save_zip + ln -s "$jda.dataset.get_file_name()" "$os.path.join($history.name, $file)"; + #end if + echo "$buf$file</font></a></li>" >> $output; + #end if + #end def + + #def print_JobParameter($parameters, $ident) + #for $par in $parameters + echo "${ident}P:$par.name '$par.value'" >> $output; + #end for + #end def + + #def job_state_color($job) + #if $job.state == $job.states.OK + #return "#B0F1B0" + #elif $job.state == $job.states.RUNNING + #return "#FFFFCC" + #elif $job.state == $job.states.QUEUED + #return "#FFFFCC" + #elif $job.state == $job.states.WAITING + #return "#EEE" + #end if + #return "#F9C7C5" + #end def + + #def print_Job($job, $rules=None, $ident="") + echo "<tr bgcolor='$job_state_color($job)'>" >> $output; + echo "<td>$job.tool_id</td><td align=center>$job.exit_code</td>" >> $output; + echo "<td>" >> $output; + #for $jda in $job.input_datasets + $print_JobToDataAssociation($jda, True, $rules) + #end for + echo "</td>" >> $output; + echo "<td>" >> $output; + #for $jda in $job.output_datasets + $print_JobToDataAssociation($jda, False, $rules, True) + #end for + echo "</td>" >> $output; + #* + #for $jda in $job.input_dataset_collections + $print_JobToDataAssociation($jda) + #end for + #for $jda in $job.output_dataset_collections + $print_JobToDataAssociation($jda) + #end for + #for $jda in $job.input_library_datasets + $print_JobToDataAssociation($jda) + #end for + #for $jda in $job.output_library_datasets + $print_JobToDataAssociation($jda) + #end for + *# + #end def + + #def enum_LibraryDatasetAssociation($hda, $jobs) + #end def + + #def enum_HistoryDatasetAssociation($hda, $jobs) + #if ($use_deleted or $hda.deleted == False) and ($use_hidden or $hda.visible == True) + #set $original_hda = $hda + #for $assoc in $original_hda.creating_job_associations + #set $jobs[$assoc.job.id] = $assoc.job + #end for + #end if + #end def + + #def enum_HistoryDatasetCollectionAssociation($hdca, $jobs) + #if ($use_deleted or $hdca.deleted == False) and ($use_hidden or $hdca.visible == True) + #set $dsc = $hdca.collection + $enum_DatasetCollection($dsc, $jobs) + #end if + #end def + + #def get_output_file($file, $jda) + #if $jda.name + #if $file != "" + #set $file += "." + #end if + #set $file += $jda.name + #end if + #if $jda.dataset.extension + #if $file != "" + #set $file += "." + #end if + #set $file += $jda.dataset.extension + #end if + #return $file + #end def + + #def rename_file($file, $rep) + #for $k, $v in $rep.iteritems() + #set $file = $file.replace($k, $v) + #end for + #return $file + #end def + + #set global $history = $output.creating_job.history + echo "<html>" > $output; + echo "<head>" >> $output; + echo " <meta http-equiv='Content-Type' content='text/html; charset=utf-8' />" >> $output; + echo " <meta http-equiv='X-UA-Compatible' content='IE=Edge,chrome=1'>" >> $output; + echo " <style type='text/css'>" >> $output; + echo " .mytable, .mytable.td, .mytable.th { font-size:11pt; }" >> $output; + echo " </style>" >> $output; + echo "</head>" >> $output; + echo "<body>" >> $output; + echo "<h1>$history.name</h1>" >> $output; + + #set $order = [] + #set $conf = {} + #set $subst = {} + #set $lines = $configuration.rstrip().split('\n') + #if len($lines) > 1 or len($lines[0].rstrip()) > 0 + echo "<p>Parameters for rename<br>" >> $output; + #for $line in $lines + #set $arr = $line.split() + echo "$arr<br>" >> $output; + $order.append($arr[0]) + #set $subst[$arr[0]] = {} + #if len($arr) == 1 + #set $subst[$arr[0]]["PREFIX"] = "" + #set $conf[$arr[0]] = "PREFIX" + #elif $arr[1].startswith("PREFIX=") + #set $z = $arr[1].split("=") + #set $subst[$arr[0]]["PREFIX"] = $z[1] if len($z) > 1 else "" + #set $conf[$arr[0]] = "PREFIX" + #else + #set $conf[$arr[0]] = $arr[1].replace(".", "_0X") + #end if + #for $x in $arr[2:] + #set $y = $x.split("=") + #set $subst[$arr[0]][$y[0]] = $y[1] if len($y) > 1 else "" + #end for + #end for + #end if + + #set $jobs = {} + #for $hda in $history.datasets + $enum_HistoryDatasetAssociation($hda, $jobs) + #end for + #for $hdca in $history.dataset_collections + $enum_HistoryDatasetCollectionAssociation($hdca, $jobs) + #end for + + #set $tools = {} + #set $specified_jobs = set() + #for $job_id, $job in $jobs.iteritems() + #set $arr = $job.tool_id.split('/') + #set $tar_tid = $arr[-1] + #if $re.match(r'^[0-9\\.]+$', $arr[-1], $re.M) + #set $tar_tid = $arr[-2] + #end if + #if not $tools.has_key($tar_tid) + #set $tools[$tar_tid] = [] + #end if + $tools[$tar_tid].append($job_id) + #if $conf.has_key($tar_tid) + $specified_jobs.add($job_id) + #end if + #end for + + #set $rules = {} + #for $tar_tid in $order if len($order) > 0 else $tools.keys() + #if $tools.has_key($tar_tid) + ##echo ">$tar_tid $conf.get($tar_tid) $"|".join($subst[$tar_tid].keys())<br>" >> $output; + #for $tar_jid in $tools[$tar_tid] + #for $jda in $jobs[$tar_jid].input_datasets + #set $tar_new = None + #if $jda.dataset + #if $conf.get($tar_tid) == "PREFIX" + #set $tar_new = $subst[$tar_tid][$conf.get($tar_tid)] + #elif str($jda.name) == $conf.get($tar_tid) + #if $rules.has_key(str($jda.dataset.id)) + #set $tar_new = $rules[str($jda.dataset.id)] + #else + #set $tar_new = $jda.dataset.name + #if $tar_new.endswith(":forward") + #set $tar_new = $tar_new[:-8] + #end if + #if $tar_new.endswith(":forward") + #set $tar_new = $tar_new[:-8] + #end if + #end if + #end if + #if $tar_new != None + #break + #end if + #end if + #end for + #if $tar_new != None + #for $jda in $jobs[$tar_jid].output_datasets + #if $jda.dataset + #set $rules[str($jda.dataset.id)] = $rename_file($get_output_file($tar_new, $jda), $subst[$tar_tid]) + ##echo "[$tar_new | $jda.dataset.id | $rules[str($jda.dataset.id)]]<br>" >> $output; + #end if + #end for + #end if + #end for + #end if + #end for + + #if $save_zip + mkdir "$history.name"; + #end if + + echo "<p><table border=1 cellpadding=2 bgcolor=#DFE5F9 style='mytable'>" >> $output; + echo "<tr><th align=center>Tool</th><th align=center>EC</th><th align=center>Input</th><th align=center>Output</th>" >> $output; + #for $job_id, $job in $jobs.iteritems() + #if $job_id != $output.creating_job.id and (not $use_specified or $job_id in $specified_jobs) + $print_Job($job, $rules) + #end if + #end for + echo "</table>" >> $output; + echo "</body>" >> $output; + echo "</html>" >> $output; + + #if $save_zip + rm $zip_file; zip -r $zip_file "$history.name"; + #end if + ]]></command> + <inputs> + <param name="use_hidden" label='Include hidden contents' type="boolean" truevalue="True" falsevalue="" checked="True" /> + <param name="use_deleted" label='Include deleted contents' type="boolean" truevalue="True" falsevalue="" /> + <param name="use_specified" label='List only specified tools below' type="boolean" truevalue="True" falsevalue="" checked="True" /> + <param name="configuration" label='Specify tool, input parameter, and substitution rules to rename output files' type="text" area="True" /> + <param name="save_zip" label='Save all output files to a zip file' type="boolean" truevalue="True" falsevalue="" /> + <param name="dummy" label='Dummy input for workflows' type="data" /> + </inputs> + <outputs> + <data format="html" name="output" label="${tool.name}: html"/> + <data format="zip" name="zip_file" label="${tool.name}: zip"> + <filter>save_zip == True</filter> + </data> + </outputs> + <help><![CDATA[ + +**Syntax of configuration** :: + + Column 1 - tool name + Column 2 - input parameter name + Column 3 or more - substitution rules in the format of match, match=, or match=replacement + +**Example** :: + + tophat2 input1 + cufflinks input .accepted_hits.bam tabular=txt + cuffquant samples.sample accepted_hits.bam.out_file=quan + cuffnorm PREFIX=cuffnorm tabular=txt + cuffdiff + +- 'input1', 'input', and 'samples.sample' are used to rename output files of 'tophat2', 'cufflinks', and 'cuffquant', respectively. +- 'PREFIX' for cuffnorm generates the original output files with a specified prefix. +- For cuffdff, the original file names are used. +- From the output file names of cufflinks '.accepted_hits.bam' is removed and 'tabular' is replaced by 'txt'. +- From the output file names of cuffquant 'accepted_hits.bam.out_file' is replaced by 'quan'. + +**Output** + ++-------------------------------------+----+----------------------------------------------+---------------------------------------+ +| Tool | EC | Input | Output | ++=====================================+====+==============================================+=======================================+ +| toolshed.g2.bx.psu.edu/repos/ | 0 | - input1: hgrna1:forward | - hgrna1.align_summary.txt | +| devteam/tophat2/tophat2/0.7 | | - input2: hgrna1:reverse | - hgrna1.insertions.bed | +| | | - gene_annotation_model: hg19dip.ensembl.gtf | - hgrna1.deletions.bed | +| | | | - hgrna1.junctions.bed | +| | | | - hgrna1.accepted_hits.bam | ++-------------------------------------+----+----------------------------------------------+---------------------------------------+ +| toolshed.g2.bx.psu.edu/repos/ | 1 | - input: hgrna1.accepted_hits.bam | - hgrna1.genes_expression.txt | +| devteam/cufflinks/cufflinks/2.2.1.0 | | - reference_annotation_guide_file: | - hgrna1.transcripts_expression.txt | +| | | hg19dip.ensembl.gtf | - hgrna1.assembled_isoforms.gtf | +| | | - ref_file: hg19dip.fa | - hgrna1.total_map_mass.txt | +| | | - global_model: hg19dip.ensembl.gtf | - hgrna1.skipped.gtf | ++-------------------------------------+----+----------------------------------------------+---------------------------------------+ +| toolshed.g2.bx.psu.edu/repos/ | 0 | - gtf_input: hg19dip.ensembl.gtf | - hgrna1.quan.cxb | +| devteam/cuffquant/cuffquant/2.2.1.0 | | - samples_0Xsample: hgrna1.accepted_hits.bam | | +| | | - ref_file: hg19dip.fa | | ++-------------------------------------+----+----------------------------------------------+---------------------------------------+ +| toolshed.g2.bx.psu.edu/repos/ | 0 | - gtf_input: hg19dip.ensembl.gtf | - cuffnorm.cds_fpkm_table.txt | +| devteam/cuffquant/cuffnorm/2.2.1.0 | | - conditionss_0Xsamples: hgrna1.quan.cxb | - cuffnorm.cds_count_table.txt | +| | | - conditionss_1Xsamples: hgrna2.quan.cxb | - cuffnorm.tss_groups_fpkm_table.txt | +| | | | - cuffnorm.tss_groups_count_table.txt | +| | | | - cuffnorm.genes_fpkm_table.txt | +| | | | - cuffnorm.genes_count_table.txt | +| | | | - cuffnorm.isoforms_fpkm_table.txt | +| | | | - cuffnorm.isoforms_count_table.txt | ++-------------------------------------+----+----------------------------------------------+---------------------------------------+ +| toolshed.g2.bx.psu.edu/repos/ | 0 | - gtf_input: hg19dip.ensembl.gtf | - splicing_diff.tabular | +| devteam/cuffquant/cuffdiff/2.2.1.2 | | - conditionss_0Xsamples: hgrna1.quan.cxb | - promoters_diff.tabular | +| | | - conditionss_1Xsamples: hgrna2.quan.cxb | - cds_diff.tabular | +| | | - ref_file: hg19dip.fa | - cds_exp_fpkm_tracking.tabular | +| | | | - cds_fpkm_tracking.tabular | +| | | | - cds_count_tracking.tabular | +| | | | - tss_groups_exp.tabular | +| | | | - tss_groups_fpkm_tracking.tabular | +| | | | - tss_groups_count_tracking.tabular | +| | | | - genes_exp.tabular | +| | | | - genes_fpkm_tracking.tabular | +| | | | - genes_count_tracking.tabular | +| | | | - isoforms_exp.tabular | +| | | | - isoforms_fpkm_tracking.tabular | +| | | | - isoforms_count_tracking.tabular | +| | | | - output_cummerbund.sqlite | ++-------------------------------------+----+----------------------------------------------+---------------------------------------+ + + ]]></help> +</tool>